Compositions and Methods of Producing Methionine

ABSTRACT

Described herein are microorganisms that produce methionine and related products from endogenous genes in a transsulfuration pathway, as well as from exogenous genes providing a direct sulfhydrylation pathway. Novel genes that are useful for methionine and SAMe production are disclosed.

FIELD

Disclosed are compositions, such as microorganisms, enzymes, andchemicals, as well as methods for using the same for producingmethionine and related products.

BACKGROUND

Methionine is an essential amino acid in the animal diet. Methionine hasbeen produced synthetically for an extensive period of time by variousmulti-step chemical synthesis employing acrolein, methyl mercaptan andcyanide as starting materials. There are two product forms:D,L-methionine and its hydroxyanalog. D-methionine is converted into therequired L-isomer in vivo, unlike all other amino acids. The market forfeed-grade methionine has been reported to be improving due to increaseddemand in poultry and more recently swine feed supplementation. Theability of the leading methionine producers (Degussa AG, Adisseo, andNovus) to meet the market demand hinges on raw material supplies. Theintermediates acrolein and methyl mercaptan must be converted into3-methylthiopropionaldelnyde (MMP) and further into methionine usinghydrogen cyanide. All three producers have plans for expansion of theirmethionine production facilities and integration with raw materialproduction as well (Chem. Marketing Reporter Apr. 7, 2003).

The biosynthetic pathways for methionine (a member of the aspartatefamily of amino acids) have been studied in a number of organisms andshow similarities as well as differences. The first dedicated step,acylation of homoserine is catalyzed by homoserine acyltransferase, andis ubiquitous in all organisms despite differences in the transferredacyl group. The product of metA catalysis is either acetylhomoserine orsuccinylhomoserine. Acylhomoserine is then converted to homocysteine viaa transsulfuration or a direct sulfhydrylation pathway. Both pathwayshave been reported to be present and functional in yeast, fungi, greenplants and the bacterium Corynebacterium glutarnicum, E. coli possessesonly the transsulfuration pathway. The transsulfuration pathway goesthrough cystathionine as an intermediate and utilizes cysteine as asulfur donor. The direct sulfhydrylation pathway involves the directincorporation of sulfide to the acylhomoserine. The last step in thepathway involves the conversion of homocysteine to methionine catalyzedby an homocysteine methyltransferase, encoded by the matE or metH genes.

Other important amino acids, such as lysine, threonine, and tryptophanare produced via fermentation for use in animal feed. Therefore, theseamino acids can be made using glucose and other renewable resources asstarting materials. Unfortunately, the production of methionine viafermentation has not been as successful and the chemical synthesis ofmethionine is still used today. This is in part due to the lack of anefficient engineered biosynthetic pathway for methionine production, anda suitable production host.

The following disclosure provides an improved methionine biosyntheticpathway, as well as production host.

SUMMARY

The production of methionine and related products, such asS-adenosylmethionine (SAMe), by fermentation are described herein.Microorganisms that have been genetically engineered to includerecombinant DNA molecules and produce methionine are also described.

A microorganism that includes an exogenous nucleic acid sequenceencoding a peptide having direct sulfhydrylation activity (EC 2.5.1.49,EC 4.2.99-), and endogenous nucleic acid sequences encoding peptideshaving transsulfuration activity (EC 2.5.1.48 and 4.4.1.8) is described.This microorganism can produce methionine and related products. In someexamples, the microorganism can have at least 0.1, 1, 2, 5, 10, 50, 75,90, or at least 100 WI, extracellular concentration of methionine orSAMe.

In some examples, the presence of more than one methionine biosyntheticpathway allows the organism to produce more methionine than would beproduced in the absence of the exogenous nucleic acid sequence encodingthe peptide having direct sulfhydrylation activity.

In other examples, more than two methionine biosynthetic pathways can beactive in the organism. In these examples one or more exogenous nucleicacid sequences encode for peptides having direct sulfhydrylationactivity. One of these peptides can use O-succinylhomoserine as asubstrate and another peptide can use O-acetylhomoserine as a substrate.

In some examples, the microorganisms engineered to make methionine andrelated products, such as SAMe, produce at least 10% of the methioninefrom transsulfuration biosynthetic pathway activity. In other examplesthey produce at least 20, 30, 40, or at least 50% of the product fromthe transsulfuration biosynthetic pathway activity.

In some examples, the microorganisms engineered to make methionine andrelated products, such as SAMe, produce at least 10% of the methioninefrom direct sulfhydrylation biosynthetic pathway activity. In otherexamples they produce at least 20, 30, 40, or at least 50% of theproduct from the direct sulfhydrylation biosynthetic pathway activity.

In some examples, the microorganism engineered to make methionine andrelated products additionally has been engineered to attenuate theactivity of a peptide encoded by a gene such as metD, metK, metJ, thrB,serA or combinations thereof. In other examples, the microorganism isadditionally engineered to over express one or more genes, such as themetA, metB, metC, metE, metY, metZ, metX, metH, cysPWUA, cysD, cysN,cysC, cysH, cysI, cysJ, cysG, csyK and cysM genes.

Methods of making methionine and SAMe are also provided. These methodsinclude culturing the microorganism engineered to make methionine andrelated products and isolating the products. In some examples themicroorganism can be E. coli, Pseudomonas sp., or Corynebacteriumglutamicum.

Also described herein are novel nucleic acid sequences and theircorresponding amino acid sequences (SEQ ID NOS: 1 and 2). These nucleicacid sequences, as well as fragments and variants of these nucleic acidsequences, are useful for producing peptides in recombinantmicroorganisms. The peptides are useful, inter alia, for producingmethionine and SAMe. The peptides, variants thereof, and fragmentsthereof, are also useful for producing specific binding agents such asantibodies.

A method of improving sulfur assimilation by bypassing thephosphoadenylylsulfate (PAPS) intermediate is also disclosed. Thismethod can be used with any microorganism used to produce methionine.The method is accomplished by introducing into a microorganism arecombinant nucleic acid sequence that allows for the over expression ofone or more adenylyl sulfate reductases (EC 1.8.9.92 or 1.8.4.9). Overexpression can be from introducing recombinant nucleic acid sequencesaltering or introducing new control elements, such as promoters orenhancers, that cause an increase in the production of endogenousadenylyl sulfate reductase or the recombinant nucleic acid sequence canencode adenylyl sulfate reductase.

These and other aspects of the disclosure are apparent from thefollowing detailed description and illustrative examples.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. is a diagram showing three general pathways used by variousmicroorganisms to produce methionine. All of the pathways rely in partupon the use of aspartate as a precursor for methionine production.Aspartate is converted through multiple steps to homoserine, homoserineis converted to O-acetyl homoserine or O-succinyl homoserine by MetA orMetX. Some microorganisms, such as E. coli and Pseudomonas sp. utilizeMetA polypeptides to make O-succinyl homoserine while othermicroorganisms such as Corynebacterium and Leptospira sp. use MetX tomake O-acetyl homoserine. O-succinyl homoserine and O-acetyl homoserinecan be then either directly converted to homocysteine throughsulfhydrylation, or they can be converted to homocysteine throughtranssulfuration (both of which reactions are described in more detailherein). Enzymes associated with transsulfuration are identified withtwo asterisks (**), and enzymes associated with sulfhydrylation areidentified with a single asterisk (*).

FIG. 2 is a graph showing accumulation of methionine in TF4076BJF, withonly transsulfuration activity (TF4076BJF), only sulfhydrylationactivity (TF4076BJF-A), or both simultaneously (TF4076BJF metYX(Lm).

FIG. 3 shows a schematic representation of the screening methodologyused to identify metA mutants that are resistant to feed backinhibition. (The product accumulated in each case is shown in theshadowed oval).

FIG. 4 shows a time course of methionine accumulation produced by astrain expressing feedback inhibition resistant metA genes.

FIG. 5 shows a model of methionine transport in E. coli.

FIG. 6 shows the native sulfur assimilation pathway and a novelalternative one.

SEQUENCE LISTING

The nucleic and amino acid sequences listed in the accompanying sequencelisting are shown using standard letter abbreviations for nucleotidebases, and threes letter code for amino acids. Only one strand of eachnucleic acid sequence is shown, but the complementary strand isunderstood as included by any reference to the displayed strand.

SEQ ID NOS: 1-10 show nucleic acid sequences and corresponding aminoacid sequences of various mutant metA genes derived from E. coli.

SEQ ID NOS: 11 through 34 show various primer sequences used in theExamples.

DETAILED DESCRIPTION Abbreviations and Terms

The following explanations of terms and methods are provided to betterdescribe the present disclosure and to guide those of ordinary skill inthe art in the practice of the present disclosure. As used herein,“comprising” means “including” and the singular forms “a” or “an” or“the” include plural references unless the context clearly dictatesotherwise. For example, reference to “comprising a cell” includes one ora plurality of such cells, and reference to “comprising the homocysteinesynthase peptide” includes reference to one or more homocysteinesynthase peptides and equivalents thereof known to those of ordinaryskill in the art, and so forth. The term “or” refers to a single elementof stated alternative elements or a combination of two or more elements,unless the context clearly indicates otherwise. For example, the phrase“homocysteine synthase activity or cystathionine γ-synthase activity”refers to homocysteine synthase activity, cystathionine γ-synthaseactivity, or a combination of both homocysteine synthase activity, andcystathionine γ-synthase activity.

Unless explained otherwise, all technical and scientific terms usedherein have the same meaning as commonly understood to one of ordinaryskill in the art to which this disclosure belongs. Although methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of the present disclosure, suitable methods andmaterials are described below. The materials, methods, and examples areillustrative only and not intended to be limiting. Other features andadvantages of the disclosure are apparent from the following detaileddescription and the claims.

Accession Numbers: The accession numbers throughout this description arederived from the NCBI database (National Center for BiotechnologyInformation) maintained by the National Institute of Health, U.S.A. Theaccession numbers are as provided in the database on Feb. 20, 2007.

Enzyme Classification numbers (EC.): The EC numbers provided throughoutthis description are derived from the KEGG Ligand database, maintainedby the Kyoto Encyclopedia of Genes and Genomics, sponsored in part bythe University of Tokyo. The EC numbers are as provided in the databaseon Feb. 20, 2007.

Attenuate: To lessen the impact, activity or strength of something. Inone example, the sensitivity of a particular enzyme to feedbackinhibition or inhibition caused by a composition that is not a productor a reactant (non-pathway specific feedback) is lessened such that theenzyme activity is not impacted by the presence of a compound. Forexample, the metA gene and its corresponding amino acid sequence (suchas the exemplary sequences provided in SEQ ID NOS: 2) show severalmutations that attenuate its feedback inhibition sensitivity. Theattenuation of MetA sensitivity is described in more detail in Example3.B. In another example, an enzyme that is less active can be referredto as attenuated.

cDNA (complementary DNA): A piece of DNA lacking internal, non-codingsegments (introns) and regulatory sequences which determinetranscription. cDNA can be synthesized by reverse transcription frommessenger RNA extracted from cells.

Deletion: The removal of one or more nucleotides from a nucleic acidmolecule or one or more amino acids from a protein, the regions oneither side being joined together.

Detectable: Capable of having an existence or presence ascertained. Forexample, production of a product from a reactant, for example, theproduction of O-succinylhomoserine or homocysteine, is detectable if thesignal generated from the product or the reactant is strong enough to bemeasured.

Direct sulfhydrylation activity: the ability to react OSHS or OAHSdirectly with S²⁻ to produce homocysteine. Peptides having this activityinclude for example, homocysteine synthases (EC 4.2.99.-, EC 2.5.1.49)which are encoded by genes such as metZ and metY.

DNA: Deoxyribonucleic acid. DNA is a long chain polymer which includesthe genetic material of most living organisms (some viruses have genesincluding ribonucleic acid, RNA). The repeating units in DNA polymersare four different nucleotides, each of which includes one of the fourbases, adenine, guanine, cytosine and thymine hound to a deoxyribosesugar to which a phosphate group is attached, Triplets of nucleotides,referred to as codons, in DNA molecules code for amino acid in apeptide. The term codon is also used for the corresponding (andcomplementary) sequences of three nucleotides in the mRNA into which theDNA sequence is transcribed.

Endogenous: As used herein with reference to a nucleic acid molecule anda particular cell or microorganism refers to a nucleic acid sequence orpeptide that is in the cell and was not placed in the cell usingrecombinant engineering techniques. For example, a gene that was in thecell when the cell was originally isolated from nature. A gene is stillconsidered endogenous if the control sequences, such as a promoter orenhancer sequences that activate transcription or translation have beenaltered through recombinant techniques.

Exogenous: As used herein with reference to a nucleic acid molecule anda particular cell refers to any nucleic acid molecule that does notoriginate from that particular cell as found in nature. Thus, anon-naturally-occurring nucleic acid molecule is considered to beexogenous to a cell once introduced into the cell. A nucleic acidmolecule that is naturally-occurring also can be exogenous to aparticular cell. For example, an entire coding sequence isolated fromcell X is an exogenous nucleic acid with respect to cell Y once thatcoding sequence is introduced ink) cell Y, even if X and Y are the samecell type.

Expression: The process by which a gene's coded information is convertedinto the structures and functions of a cell, such as a protein, transferRNA, or ribosomal RNA. Expressed genes include those that aretranscribed into mRNA and then translated into protein and those thatare transcribed into RNA but not translated into protein (for example,transfer and ribosomal RNAs).

Functional Deletion: A mutation, partial or complete deletion,insertion, or other variation made to a gene sequence which reduces orinhibits production of the gene product, or renders the gene productnon-functional. For example, functional deletion of metJ in E. colireduces the repression of the methionine biosynthetic pathway. Inanother example, functional deletion of thrB in E. coli reduces the useof homoserine in the threonine biosynthetic pathway. In some instances afunctional deletion is described as a knock out mutation.

Isolated: An “isolated” biological component (such as a nucleic acidmolecule, protein, or cell) has been substantially separated or purifiedaway from other biological components in which the component naturallyoccurs, such as other chromosomal and extrachromosomal DNA and RNA, andproteins. Nucleic acid molecules and proteins that have been “isolated”include nucleic acid molecules and proteins purified by standardpurification methods. The term also embraces nucleic acid molecules andproteins prepared by recombinant expression in a host cell as well aschemically synthesized nucleic acid molecules and proteins.

In one example, isolated refers to a naturally-occurring nucleic acidmolecule that is not immediately contiguous with both of the sequenceswith which it is immediately contiguous (one on the 5′ end and one onthe 3′ end) in the naturally-occurring genome of the organism from whichit is derived.

Nucleic acid molecule: Encompasses both RNA and DNA molecules including,without limitation, cDNA, genomic DNA, and mRNA. Includes syntheticnucleic acid molecules, such as those that are chemically synthesized orrecombinantly produced. The nucleic acid molecule can be double-strandedor single-stranded. Where single-stranded, the nucleic acid molecule canbe the sense strand or the antisense strand. In addition, nucleic acidmolecule can be circular or linear.

Operably linked: A first nucleic acid sequence is operably linked with asecond nucleic acid sequence when the first nucleic acid sequence isplaced in a functional relationship with the second nucleic acidsequence. For instance, a promoter is operably linked to a codingsequence if the promoter affects the transcription or expression of thecoding sequence. Generally, operably linked DNA sequences are contiguousand, where necessary to join two protein coding regions, in the samereading frame. Configurations of separate genes that are transcribed intandem as a single messenger RNA are denoted as operons. Thus placinggenes in close proximity, for example in a plasmid vector, under thetranscriptional regulation of a single promoter, constitutes a syntheticoperon.

ORF (open reading frame): A series of nucleotide triplets (codons)coding for peptides, polypeptides or amino acids without any terminationcodon. These sequences are usually translatable into a peptide.

Purified: The term purified does not require absolute purity; rather, itis intended as a relative term. Thus, for example, a purified peptidepreparation, such as a succinylCoA homoserine acyltransferase, or ahomocysteine synthase preparation, is one in which the peptide is moreconcentrated than the peptide is in its environment within a cell. Forexample, a purified peptide is one that is substantially separated fromcellular components (nucleic acids, lipids, carbohydrates, and otherpeptides) that may accompany it. In another example, a purified peptidepreparation is one in which the peptide is substantially-free fromcontaminants, such as those that might be present following chemicalsynthesis of the peptide.

In one example, a peptide is purified when at least about 50% by weightof a sample is composed of the peptide, for example when at least about60%, 70%, 80%, 85%, 90%, 92%, 95%, 98%, or 99% or more of a sample iscomposed of the peptide. Examples of methods that can be used to purifya peptide, include, but are not limited to the methods disclosed inSambrook et al. (Molecular Cloning: A Laboratory Manual, Cold SpringHarbor, N.Y., 1989, Ch. 17). Protein purity can be determined by, forexample, polyacrylamide gel electrophoresis of a protein sample,followed by visualization of a single peptide band upon staining thepolyacrylamide gel; high-pressure liquid chromatography; sequencing; orother conventional methods.

Recombinant: A recombinant nucleic acid molecule or protein is one thathas a sequence that is not naturally occurring, has a sequence that ismade by an artificial combination of two otherwise separated segments ofsequence, or both. This artificial combination can be achieved, forexample, by chemical synthesis or by the artificial manipulation ofisolated segments of nucleic acid molecules or proteins, such as geneticengineering techniques. Recombinant is also used to describe nucleicacid molecules that have been artificially manipulated, but contain thesame regulatory sequences and coding regions that are found in theorganism from which the nucleic acid was isolated.

Sequence Identity/similarity: The identity/similarity between two ormore nucleic acid sequences, or two or more amino acid sequences, isexpressed in terms of the identity or similarity between the sequences.Sequence identity can be measured in terms of percentage identity; thehigher the percentage, the more identical the sequences are. Sequencesimilarity can be measured in terms of percentage similarity (whichtakes into account conservative amino acid substitutions); the higherthe percentage, the more similar the sequences are. Homologs ororthologs of nucleic acid or amino acid sequences possess a relativelyhigh degree of sequence identity/similarity when aligned using standardmethods.

Methods of alignment of sequences for comparison are well known in theart. Various programs and alignment algorithms are described in: Smith &Waterman, Adv. Appl. Math. 2:482, 1981; Needleman. & Wunsch, J. Mol.Biol. 48:443, 1970; Pearson & Lipman, Proc. Natl. Acad. Sci. USA85:2444, 1988; Higgins & Sharp, Gene, 73:237-44, 1988; Higgins & Sharp,CABIOS 5:151-3, 1989; Corpet, at al., Nuc. Acids Res. 16:10881-90, 1988;Huang at al. Computer Appls. in the Biosciences 8, 155-65, 1992; andPearson at al., Meth. Mol. Bio, 24:307-31, 1994. Altschul at al., J.Mol. Biol. 215:403-10, 1990, presents a detailed consideration ofsequence alignment methods and homology calculations.

The NCBI Basic Local Alignment Search Tool (BLAST) (Altschul at al., J.Mol. Biol. 215:403-10, 1990) is available from several sources,including the National Center for Biological Information (NCBI, NationalLibrary of Medicine, Building 38A, Room 8N805, Bethesda, Md. 20894) andon the Internet, for use in connection with the sequence analysisprograms blastp, blastn, blastx, tblastn and tblastx. Additionalinformation can be found at the NCBI web site.

BLASTN is used to compare nucleic acid sequences, while BLASTP is usedto compare amino acid sequences. To compare two nucleic acid sequences,the options can be set as follows: -i is set to a file containing thefirst nucleic acid sequence to be compared (such as C:\seq1.txt); -j isset to a file containing the second nucleic acid sequence to be compared(such as C:\seq2.txt); -p is set to blastn; -o is set to any desiredfile name (such as C:\output.txt); -q is set to −1; -r is set to 2; andall other options are left at their default setting. For example, thefollowing command can be used to generate an output file containing acomparison between two sequences: C:\B12seq-c:\seq1.txt-j c:\seq2.txt-pblastn-o c:\output.txt-q-1-r2.

To compare two amino acid sequences, the options of B12seq can be set asfollows: -i is set to a file containing the first amino acid sequence tobe compared (such as C:\seq1.txt); -j is set to a file containing thesecond amino acid sequence to be compared (such as C:\seq2.txt), -p isset to blastp; -o is set to any desired file name (such asC:\output.txt); and all other options are left at their default setting.For example, the following command can be used to generate an outputfile containing a comparison between two amino acid sequences:C:\B12seq-i c:\seq1.txt-j c:\seq2.txt-p blastp-o c:\output.txt. If thetwo compared sequences share homology, then the designated output filewill present those regions of homology as aligned sequences. If the twocompared sequences do not share homology, then the designated outputfile will not present aligned sequences.

Once aligned, the number of matches is determined by counting the numberof positions where an identical nucleotide or amino acid residue ispresented in both sequences. The percent sequence identity is determinedby dividing the number of matches either by the length of the sequenceset forth in the identified sequence, or by an articulated length (suchas 100 consecutive nucleotides or amino acid residues from a sequenceset forth in an identified sequence), followed by multiplying theresulting value by 100. For example, a nucleic acid sequence that has1166 matches when aligned with a test sequence having 1554 nucleotidesis 75.0 percent identical to the test sequence (1166÷1554*100=75.0). Thepercent sequence identity value is rounded to the nearest tenth. Forexample, 75.11, 75.12, 75.13, and 75.14 are rounded down to 75.1, while75.15, 75.16, 75.17, 75.18, and 75.19 are rounded up to 75.2. The lengthvalue will always be an integer.

For comparisons of amino acid sequences of greater than about 30 aminoacids, the Blast 2 sequences function is employed using the defaultBLOSUM62 matrix set to default parameters, (gap existence cost of 11,and a per residue gap cost of 1). Homologs are typically characterizedby possession of at least 70% sequence identity counted over thefull-length alignment with an amino acid sequence using the NCBI BasicBlast 2.0, gapped blastp with databases such as the nr or swissprotdatabase. Queries searched with the blastn program are filtered withDUST (Hancock and Armstrong, 1994, Comput. Appl. Biosci. 10:67-70).Other programs use SEG. In addition, a manual alignment can beperformed. Proteins with even greater similarity will show increasingpercentage identities when assessed by this method, such as at least75%, at least 80%, at least 85%, at least 90%, at least 95%, at least97%, or at least 99% sequence identity to the subject sequence (i.e.sequence identified by accession number or the like), while retainingthe activity of the subject sequence. In some examples, the subjectsequence will have greater activity than that of the native sequence andin yet other examples it will be less active.

When aligning short peptides (fewer than approximately 30 amino acids),the alignment should be performed using the Blast 2 sequences function,employing the PAM30 matrix set to default parameters (open gap 9,extension gap 1 penalties). Proteins with even greater similarity to thereference sequence will show increasing percentage identities whenassessed by this method, such as at least 60%, 70%, 75%, 80%, 85%, 90%,95%, 98%, 99% sequence identity. When less than the entire sequence isbeing compared for sequence identity, homologs will typically possess atleast 75% sequence identity over short windows of 10-20 amino acids, andcan possess sequence identities of at least 85%, 90%, 95% or 98%depending on their identity to the reference sequence. Methods fordetermining sequence identity over such short windows are described atthe NCBI web site.

Nucleic acid sequences that do not show a high degree of identity maynevertheless encode identical or similar (conserved) amino acidsequences, due to the degeneracy of the genetic code. Changes in anucleic acid sequence can be made using this degeneracy to producemultiple nucleic acid molecules that all encode substantially the sameprotein. Such homologous nucleic acid sequences can, for example,possess at least 60%, at least 70%, at least 80%, at least 90%, at least95%, at least 98%, or at least 99% sequence identity to a subjectsequence (sequences identified by accession number or the like).

One of skill in the art will appreciate that these sequence identityranges are provided for guidance only; it is possible that stronglysignificant homologs could be obtained that fall outside the rangesprovided.

Transformed cell: A cell into which a nucleic acid molecule has beenintroduced, such as a succinylCoA homoserine acyltransferase, or ahomocysteine synthase nucleic acid molecule, for example by molecularbiology techniques. Transformation encompasses all techniques by which anucleic acid molecule can be introduced into such a cell, including, butnot limited to, transfection with viral vectors, conjugation,transformation with plasmid vectors, and introduction of naked DNA byelectroporation, lipofection, and particle gun acceleration.

Transsulfuration activity: An activity that produces methionine or SAMevia the intermediate, cystathionine. Peptides having this activityinclude cystathionine γ synthase (EC 2.5.1.48) and cystathionine β lyase(EC 4.4.1.8), these peptides are encoded by the genes metB and metC,respectively. Any combination of cystathionine γ synthase (EC 4.2.99.9)and cystathionine β lyase (EC 4.4.1.8) peptides can be used to allow amicroorganism to possess transsulfuration activity.

Under conditions that permit product production: Any fermentationconditions that allow a microorganism to produce a desired product, suchas methionine or SAMe. Conditions usually include temperature, aeration,and medium. The medium can be a broth or a gel. Generally, the mediumincludes a carbon source such as glucose, fructose, cellulose, or thelike that can be metabolized by the microorganism directly, or enzymescan be used in the medium to facilitate metabolizing the carbon source.To determine if culture conditions permit product production, themicroorganism can be cultured for 24, 36, or 48 hours and a sample canbe taken. The cells in the sample can be then tested for the presence ofthe desired product. For example when testing for the presence ofmethionine car SAMe the assays provided in the Examples section may beused.

Vector: A nucleic acid molecule as introduced into a cell, therebyproducing a transformed cell. A vector can include nucleic acidsequences that permit it to replicate in the cell, such as an origin ofreplication. A vector can also include one or more selectable markergenes and other genetic elements known in the art.

DETAILED DESCRIPTION I. Methionine Production Pathways

As shown in FIG. 1, many biosynthetic pathways can be used to producemethionine or its intermediates such as aspartyl phosphate, aspartatesemialdehyde homoserine, O-succinylhomoserine (OSHS), O-acetylhomoserine(OAHS), cystathionine, homocysteine, methionine, and S-adenosylmethionine (SAMe). For the purposes of this disclosure an intermediatecan be referred to as a reactant or a product, depending upon context.For example, when discussing the conversion of aspartate to aspartylphosphate using an aspartate kinase, the aspartate is the reactant andthe aspartyl phosphate is the product. Similarly, when the descriptiondescribes the conversion of aspartyl phosphate to aspartate semialdehydeusing an aspatate semialdehyde dehydrogenase, the aspartyl phosphate isthe reactant and the aspartate semialdehyde is the product. One ofordinary skill in the art will appreciate that FIG. 1 shows manybiosynthetic pathways because within each enzyme class provided thereare many enzymes that can be used to convert a reactant to a productand, therefore, make a pathway. Moreover, these reactions can be carriedout in vivo, in vitro, or through a combination of in vivo reactions andin vitro reactions, such as in vitro reactions that includenon-enzymatic chemical reactions.

The host microorganism can also be provided intermediates in the pathwayby including the intermediates in the fermentation feedstock. Thus, ifthe biosynthetic pathway is producing less than a desired amount of agiven intermediate, that intermediate can be added to the feedstock.This can be done in either a continuous fermentation setting or in abatch fermentation setting.

Those of ordinary skill in the art will recognize that a production hostcan use carbon sources other than glucose. Alternative carbons sourcesinclude for example, sucrose, fructose, cellulose, hemicellulose,starch, or glycerol. When alternative carbon sources are used it may benecessary to include enzymes that will modify the carbon source in thefermentation media.

A. Glucose to Aspartate

Microorganisms generally produce aspartate from glucose. One of ordinaryskill in the art will appreciate that there are many methods ofincreasing the aspartate concentration in production strains. Forexample, increasing the expression of the enzymes pyruvate carboxylaseand phosphoenolpyruvate carboxylase, altering the glyoxylate shunt oreliminating the consumption of pyruvate into other products such asacetate or ethanol.

Alternatively, aspartate can be included in the fermentation feedstock,taken up by the microorganism, and used as a reactant in the methioninebiosynthetic pathway.

Aspartate also serves as an intermediate in the lysine, threonine, andasparagine biosynthetic pathways. Therefore, it may be desirable toattenuate or remove (knockout) these pathways, thus allowing moreaspartate to be used in the methionine production pathway.

B. Aspartate to Aspartyl Phosphate

Production hosts can be engineered using known polypeptides to produceaspartyl phosphate, or to overproduce aspartyl phosphate. For example,the feed back resistant aspartate kinase described in WO04069996A2 canbe used to replace an endogenous aspartate kinase or in addition to anendogenous aspartate kinase.

As used herein, aspartate kinase includes peptides in enzymeclassification number (BC) 2.7.2.4, as well as any other peptide capableof catalyzing the conversion of aspartate to aspartyl phosphate.Additionally, one of ordinary skill in the art will appreciate that someaspartate kinase peptides will catalyse other reactions as well, forexample some aspartate kinase peptides will accept other substrates inaddition to aspartate. Such non-specific aspartate kinase peptides are,therefore, also included. Aspartate kinase sequences are publiclyavailable. For example, GenBank Accession Nos: NZ_AAVY01000022,NC_(—)006958, and NZ_AAWW01000055, disclose aspartate kinase nucleicacid sequences and GenBank Accession Nos: NP_(—)418448, NP_(—)599504 andZP_(—)01638096 disclose aspartate kinase peptide sequences. Assays forcharacterizing the aspartate kinase activity of a particular peptide arewell known in the art. For example, the assay described by Cohen, GN,Methods in Enzymology, 113:596:600, 1985, can be used to characterizethe activity of a specific peptide.

C. Aspartyl Phosphate to Aspartate Semialdehyde

Production hosts can be engineered using known polypeptides to produceaspartate semialdehyde, or to overproduce aspartate semialdehyde. Onemethod of increasing the production of products in the methioninebiosynthetic pathway is through over-expression or the expression of amore active form of aspartate semialdehyde dehydrogenase.

As used herein, aspartate semialdehyde dehydrogenase includes aspartatesemialdehyde dehydrogenase peptides (EC 1.2.1.11), as well as any otherpeptide capable of catalyzing the conversion of aspartyl phosphate toaspartate semialdehyde. Additionally, one of ordinary skill in the artwill appreciate that some aspartate semi aldehyde dehydrogenase peptideswill catalyze ether reactions as well. For example, some aspartatesemialdehyde dehydrogenase peptides will accept other substrates inaddition to aspartyl phosphate, and therefore, such non-specificaspartate semialdehyde dehydrogenase peptides are also included.Aspartate semialdehyde dehydrogenase sequences are publicly available.For example, GenBank Accession Nos: NC_(—)006958, NZ_AAVY01000015 andNZ_AAWW01000010 disclose aspartate semialdehyde dehydrogenase nucleicacid sequences and GenBank Accession Nos: NP_(—)417891, NP_(—)599505 andZP_(—)0164))72 disclose aspartate semialdehyde dehydrogenase peptidesequences. Assays for characterizing the aspartate semialdehydedehydrogenase activity of a particular peptide are well known in theart. For example, the assay described by Cohen, G N., Methods inEnzymology, 113:600-602, 1985, can be used to characterize the activityof a specific peptide.

D. Aspartate Semialdehyde to Homoserine

Production hosts can be engineered using to polypeptides to producehomoserine, or to overproduce homoserine. One method of increasing theproduction of products in the methionine biosynthetic pathway is throughover expression or the expression of a more active form of aspartatesemialdehyde dehydrogenase.

As used herein, homoserine dehydrogenase includes homoserinedehydrogenase peptides (EC 1.1.1.3), as well as any other peptidecapable of catalyzing the conversion of aspartate semialdehyde tohomoserine. Additionally, one of ordinary skill in the art willappreciate that some homoserine dehydrogenase peptides will catalyzeother reactions as well, for example some homoserine dehydrogenasepeptides will accept other substrates in addition to aspartatesemialdehyde. Such non-specific homoserine dehydrogenase peptides are,therefore, also included. Homoserine dehydrogenase peptide sequences arepublicly available. For example, GenBank Accession Nos: NC_(—)006958,NZ_AAVY01000013 and NZ_AAWW01000033 disclose homoserine dehydrogenasenucleic acid sequences and GenBank Accession Nos: NP_(—)414543,ZP_(—)01639819 and NP_(—)600409 disclose homoserine dehydrogenasepeptide sequences. Assays for characterizing the homoserinedehydrogenase activity of a particular peptide are well known in theart. For example, the assay described by Patte et. al., Biochem.Biophys. Acta 121:426-439, 1966, can be used to characterize theactivity of a specific peptide.

E. Homoserine to O-Succinylhomoserine (OSHS)

Production hosts can be engineered using known polypeptides to produceO-succinylhomoserine (OSHS), or to overproduce OSHS. One method ofincreasing the production of products in the methionine biosyntheticpathway is through over expression or the expression of a more activeform of homoserine O-succinyltransferase peptides, or using a feed backinhibition insensitive form of homoserine O-succinyltransferasepeptides.

As used herein, succinylCoA homoserine acyltransferase, includeshomoserine O-succinyltransferase peptides (BC 2.3.1.46), as well as anyother peptide capable of catalyzing the conversion of homoserine toOSHS. Additionally, one of ordinary skill in the art will appreciatethat some homoserine O-succinyltransferase peptides will catalyze otherreactions as well, for example some succinylCoA-homoserineacyltransferase peptides will accept other substrates in addition tohomoserine. Such non-specific succinylCoA-homoserine acyltransferasepeptides are, therefore, also included. Homoserine O-succinyltransferasepeptide sequences are publicly available. For example, GenBank AccessionNo: NZ_AAWW01000055 discloses a homoserine O-succinyltransferase nucleicacid sequence and GenBank Accession No: AAC76983 discloses a homoserineO-succinyltransferase peptide sequence. Assays for characterizingsuccinylCoA-homoserine acyltransferase activity are well known in theart. For example, the assay described by Lawrence, J. Bacteriol.,109:8-11, 1972, can be used to characterize the activity of a specificpeptide. Genes encoding succinylCoA-homoserine acyltransferase peptidesare also referred to herein as metA.

F. Homoserine to O-Acetylhomoserine (OAHS)

Production hosts can be engineered using known polypeptides to produceO-acetylhomoserine (OAHS), or to overproduce OAHS. One method ofincreasing the production of products in the methionine biosyntheticpathway is through over expression or the expression of a more activeform of homoserine O-acetyltransferase peptides (EC 2.3.1.31).

As used herein, homoserine O-acetyltransferase, includes homoserineO-acetyltransferase peptides (EC 2.3.1.31), as well as any other peptidecapable of catalyzing the conversion to OAHS. Additionally, one ofordinary skill in the art will appreciate that some homoserineO-acetyltransferase peptides will catalyze other reactions as well, forexample some homoserine O-acetyltransferase peptides will accept othersubstrates in addition to homoserine. Such non-specific homoserineO-acetyltransferase peptides are, therefore, also included. HomoserineO-acetyltransferase peptide sequences are publicly available. Forexample, GenBank Accession Nos: Y10744 REGION: 2822 . . . 3961,NZ_AAAH02000004 REGION: 166057 . . . 167193 and NZ_AAAY02000081 REGION:complement (11535 . . . 12605) disclose homoserine O-acetyltransferasenucleic acid sequences and GenBank Accession Nos: CAA71733,ZP_(—)00766367 and ZP_(—)00107218 disclose homoserineO-acetyltransferase peptide sequences. Assays for characterizinghomoserine O-acetyltransferase activity are well known in the art. Forexample, the assay described by Lawrence, J. Bacteriol., 109:8-11, 1972,can be used to characterize the activity of a specific peptide. Genesencoding homoserine O-acetyltransferase peptides are also referred toherein as metX.

G. Sulfhydrylation

The production of homocysteine by direct sulfhydrylation is accomplishedby homocysteine synthase enzymes, some of these enzymes utilize OSHS asa substrate, and some of utilize OAHS as a substrate. Additionally, someof the enzymes can utilize either OSHS or OAHS as substrates.

1. O-Succinylhomoserine (OSHS) to Homocysteine

Production hosts can be engineered using known polypeptides to producehomocysteine, or to overproduce homocysteine. One method of increasingthe production of products in the methionine biosynthetic pathway isthrough over expression or the expression of a more active form ofhomocysteine synthase peptides (EC 4.2.99.-).

As used herein, homocysteine synthase includes homocysteine synthasepeptides (EC 4.2.99.-), as well as any other peptide capable ofcatalyzing the conversion of O-succinylhomoserine (OSHS) tohomocysteine. The conversion of OSHS to homocysteine through reactionwith sulfide is referred to herein as direct sulfhydrylation.Additionally, one of ordinary skill in the art will appreciate that somehomocysteine synthase peptides will catalyze other reactions as well,for example some homocysteine synthase peptides will accept othersubstrates in addition to OSHS. Such non-specific homocysteine synthasepeptides are, therefore, also included. Homocysteine synthase peptidesequences are publicly available. For example, GenBank Accession No:AE004091 discloses a homocysteine synthase (O-succynil-L-homoserinesulfhydrylase) nucleic acid sequences and GenBank Accession No: AAG06495discloses a homocysteine synthase (O-succynil-L-homoserinesulfhydrylase) amino acid sequence. Assays for characterizing thehomocysteine synthase activity of a particular peptide are well known inthe art. For example, the assay described by Yamagata, Methods inEnzymology, 143:478, 1987, can be used, with the appropriate substrate,to characterize the activity of a specific peptide. Genes encodinghomocysteine synthase peptides are also referred to herein as metZ.

2. O-Acetylhomoserine (OAHS) Homocysteine

Production hosts can be engineered using known polypeptides to producehomocysteine, or to overproduce homocysteine. One method of increasingthe production of products in the methionine biosynthetic pathway isthrough over expression or the expression of a more active form ofhomocysteine synthase peptides (EC 2.5.1.49).

As used herein, homocysteine synthase includes homocysteine synthasepeptides (EC 2.5.1.49), as well as any other peptide capable ofcatalyzing the conversion of O-succinylhomoserine (OAHS) tohomocysteine. The conversion of OAHS to homocysteine through reactionwith sulfide is referred to herein as direct sulfhydrylation.Additionally, one of ordinary skill in the art will appreciate that somehomocysteine synthase peptides will catalyze other reactions as well,for example some homocysteine synthase peptides will accept othersubstrates in addition to OSHS, for example the homocysteine synthasedescribed in Example 2, below accepts either OAHS or OSHS as asubstrate, such non-specific homocysteine synthase peptides are,therefore, also included. Homocysteine synthase peptide sequences thatare publicly available. For example, GenBank Accession Nos: AE004091REGION: 5655648 . . . 5656925, Y10744 REGION: 1485 . . . 2813,NZ_AAAH02000004 REGION: 164536 . . . 165990 and NZ_AAAY02000081 REGION:complement (12750 . . . 14054) disclose homocysteine synthase(O-acetyl-L-homoserine sulfhydrylase) nucleic acid sequences and GenBankAccession Nos: AAG08410, CAA71732, ZP_(—)00766366, and ZP_(—)00107219disclose homocysteine synthase (O-acetyl-L-homoserine sulfhydrylase)amino acid sequences. Assays for characterizing the homocysteinesynthase activity of a particular peptide are well known in the art. Forexample, the assay described by Yamagata, Methods in Enzymology,143:478, 1987, can be used, with the appropriate substrate, tocharacterize the activity of a specific peptide. Genes encodinghomocysteine synthase peptides are also referred to herein as metY.

H. Transsulfuration

1. O-Succinylhomoserine (OSHS) or Acetylhomoserine (OAHS) toCystathionine

Production hosts can be engineered using known polypeptides to producecystathionine, or to overproduce cystathionine. One method of increasingthe production of products in the methionine biosynthetic pathway isthrough over expression or the expression of a more active form ofcystathionine γ-synthase peptides (EC 2.5.1.48).

As used herein, cystathionine γ-synthase includes cystathionineγ-synthase peptides (EC 2.5.1.48), as well as any other peptide capableof catalyzing the conversion of OSHS or OARS to cystathionine.Additionally, one of ordinary skill in the art will appreciate that somecystathionine γ-synthase peptides will catalyze other reactions as well,for example some cystathionine γ-synthase peptides will accept othersubstrates in addition to OSHS or OAHS. Such non-specific cystathionineγ-synthase peptides are, therefore, also included. Cystathionineγ-synthase peptide sequences are publicly available. For example,GenBank Accession Nos: NC_(—)006958, NZ_AAWW01000006 and NC_(—)004129disclose cystathionine γ-synthase nucleic acid sequences and GenBankAccession Nos: NP_(—)418374, YP_(—)348978 and NP_(—)601979 disclosecystathionine γ-synthase peptide sequences. Assays for characterizingthe cystathionine γ-synthase activity of a particular peptide are wellknown in the art. For example, the assay described in Methods inEnzymology, 17:425-433, 1971, can be used to characterize the activityof a specific peptide. Genes encoding cystathionine γ-synthase peptidesare also referred to herein as metB.

2. Cystathionine to Homocysteine

Production hosts can be engineered using known polypeptides to producehomocysteine, or to overproduce homocysteine. One method of increasingthe production of products in the methionine biosynthetic pathway isthrough over expression or the expression of a more active form ofcystathionine β-lyase peptides (EC 4.4.1.8).

As used herein, cystathionine β-lyase includes cystathionine β-lyasepeptides (EC 4.4.1.8), as well as any other peptide capable ofcatalyzing the conversion of cystathionine to homocysteine.Additionally, one of ordinary skill in the art will appreciate that somecystathionine β-lyase peptides will catalyze other reactions as well,for example some cystathionine β-lyase peptides will accept othersubstrates in addition to cystathionine. Such non-specific cystathionineβ-lyase peptides are, therefore, also included. Cystathionine β-lyasepeptide sequences are publicly available. For example, GenBank AccessionNos: NZ_AAWW01000001, NC_(—)006958 and NZ_AAVY01000004 disclosecystathionine β-lyase nucleic acid sequences and GenBank Accession Nos:NP_(—)746463, YP_(—)226552 and NP_(—)417481 disclose cystathionineβ-lyase peptide sequences. Assays for characterizing the cystathionineβ-lyase activity of a particular peptide are well known in the art. Forexample, the assay described in Methods in Enzymology, 143:483.486,1987, can be used to characterize the activity of a specific peptide.Genes encoding cystathionine β-lyase peptides are also referred toherein as metC.

I. Homocysteine to Methionine

Production hosts can be engineered using known polypeptides to producemethionine, or to overproduce methionine. One method of increasing theproduction of products, such as methionine or SAMe in the methioninebiosynthetic pathway is through over expression or the expression of amore active form of homocysteine methlyase peptides (EC 2.1.1.14 and2.1.1.13).

As used herein, homocysteine methlyase includes homocysteine methlyasepeptides (EC 2.1.1.14, and 2.1.1.13), as well as any other peptidecapable of catalyzing the conversion of homocysteine to methionine.Additionally, one of ordinary skill in the art will appreciate that somehomocysteine methlyase peptides will catalyze other reactions as well,for example some homocysteine methlyase peptides will accept othersubstrates in addition to homocysteine. Such non-specific homocysteinemethlyase peptides are, therefore, also included, Homocysteine methlyasepeptide sequences are publicly available. For example, GenBank AccessionNos: NC_(—)004129, NC_(—)006958 and NC_(—)100913 disclose homocysteinemethlyase nucleic acid sequences and GenBank Accession Nos:AP_(—)004520, YP_(—)225791 and CAK16133 disclose homocysteine methlyasepeptide sequences. Assays for characterizing homocysteine methlyaseactivity of a particular peptide are well known in the art. For example,the assay described in Analytical Biochemistry, 228, 323-329, 1995, canbe used to characterize the activity of a specific peptide. Genesencoding homocysteine methlyase peptides are also referred to herein asmeal or metE.

J. Methionine S-Adenosylmethionine

Production hosts can be engineered using known polypeptides to produceS-adenosylmethionine (SAMe), or to overproduce SAMe. One method ofincreasing the production of products, in the methionine biosyntheticpathway is through over expression or the expression of a more activeform of methionine adenosyltransferase peptides (EC 2.5.1.6). One ofordinary skill in the art will appreciate that in instances wheremethionine is the desired product, the activity or expression ofmethionine adenosyltransferase peptides (EC 2.5.1.6) encoded by metK,may be attenuated.

As used herein, methionine adenosyltransferase includes methionineadenosyltransferase peptides (EC 2.5.1.6), as well as any other peptidecapable of catalyzing the conversion of methionine to SAMe.Additionally, one of ordinary skill in the art will appreciate that somemethionine adenosyltransferase peptides will catalyze other reactions aswell, for example some methionine adenosyltransferase peptides willaccept other substrates in addition to methionine. Such non-specific,methionine adenosyltransferase peptides are, therefore, also included.Methionine adenosyltransferase peptide sequences are publicly available.For example, GenBank Accession Nos: NC_(—)002516, NC_(—)006958 andNC_(—)000913 disclose methionine adenosyltransferase nucleic acidsequences and GenBank Accession Nos: NP_(—)747070, CAI37180 andNP_(—)600817 disclose methionine adenosyltransferase peptide sequences.Assays for characterizing the methionine adenosyltransferase activity ofa particular peptide are well known in the art. For example, the assaydescribed in Methods in Enzymology, 94: 219-222, 1983, can be used tocharacterize the activity of a specific peptide. Genes encodingmethionine adenosyltransferase peptides are also referred to herein asmetK.

II. Genetic Engineering of Production Strain to Increase MethionineProduction

Aspartate production can be increased using any method known in the art.For example, aspartate production can be increased by increasing theamount of oxaloacetate produced by the cells with several differentapproaches. (Gokarn et. al, Appl. Microbial. Bictechnol., 56:188-95,2001; Sanchez et. al, Metabolic Eng., 8:209-226, 2006).

The production of product can also be increased by over expressingvarious genes in the L-methionine biosynthetic pathway. For example,genes such as metA, metB, metC, metE, and metH, cysD, cysN, cysC, cysH,cysI, cysJ, cysK and cysM can be placed under the control of a varietyof promoters thus allowing higher amounts of these enzymes to beproduced.

The metA gene encodes homoserine succinyltransferase which is the firstenzyme in the methionine biosynthesis pathway from homoserine and aregulation point for methionine production. The metA protein is atemperature sensitive protein of 186 amino acid residues with acalculated molecular mass of 35.7 kDa. The metA activity is known to beinhibited by the end-products, methionine and S-adenosylmethionine (Leeet al., J. Biol. Chem. 241:5479-5780, 1966). Feedback inhibition bythese two products is synergistic, meaning that low concentrations ofeach metabolite alone are only slightly inhibitory, while in combinationa strong inhibition is exerted. Thus, a production strain could benefitfrom a feedback inhibition resistant MetA activity.

Another gene that can be attenuated or deleted in the methionineproduction strain is metJ. The peptide encoded by metJ regulates theexpression of several genes involved in methionine biosynthesis pathway.The protein encoded by metJ binds to S-adenosyl methionine and repressesthe metA, metC, and metF genes.

The protein encoded by the metF gene, 5,10-methylenetetrahydrofolatereductase, is involved in the synthesis of N(5)-methyltetrahydrofolatewhich is a methyl group donor for L-methionine product on fromhomocysteine (Sheppard et al., J. Bacteria 181:718-25, 1999). US2002/0049305 discloses that the production of L-methionine can beimproved by increasing the expression of 5, 10-methylenetetrahydrofolatereductase (metF) in Corynebacteria. Accordingly, the engineeredmicroorganisms described herein can also be engineered to increase metFproduction.

The modulation of the gene metK can also increase methionine and SAMeproduction. S-adenosylmethionine (SAMe) is the primary methyl groupdonor in all organisms and is involved in polyamine biosynthesis. SAMeis also known as methionine adenosyltransferase (MAT or MetK, EC2.5.1.6). MetK catalyzes the only known route for SAMe biosynthesis. Thecomplete tripolyphosphate chain is cleaved from ATP and the sulfoniumcompound is formed.

The formation of SAMe decreases the concentration of methionine andreduces the activity of the methionine biosynthetic pathway via feedback inhibition of MetA. Hence, functionally deleting or attenuatingmetK can increase methionine production.

One of ordinary skill in the art will appreciate that the efficiency ofsulfur utilization by any cell that is making methionine is important.This is especially true for microorganisms that utilizephosphoadenylylsulfate (PAPS) as an intermediate during sulfurassimilation, because making PAPS requires the expenditure of a-moleculeof ATP.

Sulfate is fairly unreactive and must first be converted to a morereactive form in order to be used by the cell. In E. coli sulfate isincorporated in the cell by a periplasmic transport system, composed ofthree cytoplasmic membrane components and a substrate specific bindingprotein located in the periplasmic space. The three membrane componentsof the sulfate permease are encoded by the cysT, cysW, and cysA genes(cysA locus). The products of the cysA locus are regulated in concertwith the rest of the sulfate-assimilation pathway as part of the cysregulon. Sulfate is then activated by coupling to a nucleoside to makehigh-energy nucleoside phosphosulfates via a pathway that appears to besimilar in most organisms.

As shown in FIG. 6, a microorganism such as E. coli utilizes a pathwaythat converts sulfate to adenylylsulfate (APS) using a sulfate adenylyltransferase peptide (EC 2.7.7.4 coded by cysNcysD). The APS is thenconverted to PAPS by APS kinase (EC 2.7.1.25 encoded by cysC). This steprequires one ATP. PAPS is converted to sulfite by a PAPS reductase (EC1.8.4.8 coded by cysH) and sulfite is reduced to sulfide byNADPH-sulfite reductase (EC 1.8.1.2 coded by cysIcysJcysG). Thealternate pathway, shown on the right side of FIG. 6, converts APSdirectly to sulfite using an adenylyl sulfate reductase (EC 1.8.9.92 or1.8.4.9). One of ordinary skill in the art will appreciate that anyadenylyl sulfate reductase that can convert APS to sulfite will work.For example, the adenylyl sulfate reductase from Bacillus subtilis(Accession number CAA04409), or from Pseudomonas aeruginosa (Accessionnumber NP_(—)250447).

Adenylyl sulfate reductase encoding nucleic acid sequences can beintroduced into any microorganism used to produce methionine. Forexample the strains described herein, as well as the strains describedin WO2005/108561 and WO2006138689 by Metabolic Explorer, and thosedescribed by Kumar and Gomes, Biotechnology Advances 23:41-61, 2005, canbenefit from the disclosed route bypassing PAPS and thus requiring oneless ATP molecule for sulfate assimilation.

EXAMPLES Example 1 Multiple Methionine Production Pathways, One of whichUtilizes Direct Sulfhydrylation, Using Exogenously Expressed NucleicAcid Sequences

A. Construction of a Microorganism Having Both MetABC (Transsulfuration)and MetAZ (Direct Sulfhydrylation)

As described before, endogenous production of methionine in E. colioccurs mainly through the transulfuration reaction. This Exampledescribes the engineering of E. coli to increase direct sulfhydrylationwhile also maintaining the endogenous metABC pathway.

Direct sulfhydrylation was increased by cloning. O-succinylsulfhydrylase(EC 4.2.99.-) which converts O-succinylhomoserine to homocysteine byreacting with hydrogen sulfide. This enzyme is codified by metZ and canbe found in some Pseudomonas species (Vermeij and Kertesz, J Bacteriol.181:5833-5837, 1999 and Inoue et al., J. Bacteria 179:3956-3962, 1997).

More specifically, metZ from Pseudomonas aeruginosa was cloned intomethionine auxotrophs of strain TF4076BJF, which was derived fromthreonine producing strain TF4076, (additionally modified by thedeletion thrB and metJ, and the insertion of metF under the control ofthe pTrc promoter, further described in Example 3, below). Theseauxotrophs have deletion of either the metes or the metB and metC genes,metZ from Pseudomonas aeruginosa enhanced the growth of the metB and themetBC deletion mutants in minimal medium. Even though in flask culturesmethionine production was not fully recovered, metZ expression inducesthe methionine production up to ˜100 mg/L in metBC deletion mutant, asshown in Table 1. This indicates that metZ is responsible for theproduction of homocysteine in the cell.

Low methionine production of the deletion mutants transformed with metZmay be due to the limitation of sulfide in the intracellular fraction(methods of increasing sulfide concentration are provided below). Thisis supported by the finding that the growth of the metBC deletion straintransformed with metZ was enhanced in M9 media in the presence of 2 mMsodium sulfide. In in-vitro assays, the O-succinylsulfhydrylase had lowsulfide affinity. Through directed evolution, it is possible to developimproved O-succinylsulfhydrylases with higher sulfide affinity and alsohigher activity. A highly active O-succinylsulfhydrylase could replacemetB and metC in the methionine pathway, or could complement the pathwayto increase the carbon flux to methionine.

TABLE 1 Growth complementation and methionine production onTF4076BFJ-ΔBC met glucose intermediate GA and HS used (mg/L) (g/L)TF4076BJF-ΔBC OD (g/L) OSH met HS GA empty vector 2.5 10.0 3867 0.0 0.00.4 pCL-metB 20.9 38.1 0.0 0.0 0.6 0.2 pCL-metB-metC 9.7 40.0 0.0 6704.36 2.4 pPro-metZ 13.0 40.0 0.0 101 3.1 4.3 pCL-metB: metB with its ownpromoter in pCL1920 pCL-metB-metC: metB and metC with their ownpromoters in pCL1920 pPro-Z: metZ from Pseudomonas aeruginosa in pProLarvector (ClonTech)

B. Construction of a Microorganism Having Both MetABC (Transsulfuration)and MetXY (Direct Sulfhydrylation)

This example shows simultaneous methionine production from two pathwaysin E. coli. One pathway is the endogenous metABC pathway and the secondpathway allows for direct sulfhydrylation via the expression of metY andmetX from various organisms.

As shown in FIG. 1 E. coli produces methionine endogenously using thetranssulfuration pathway genes metA, metB and metC and goes throughOSHS. Genetic engineering was used to add an additional pathway to E.coli by cloning and expressing the genes metX and metY into E. coli,which resulted in a host organism that makes methionine through bothtranssulfuration and direct sulfhydrylation simultaneously.

The metY and metX genes used to construct the heterologous pathway werecloned from Leptospira meyeri, Deinococcus radiodurans, Chloroflexusaurantiacus, Brevibacterium linens, Nostoc punctiforme and Pseudomonasaeruginosa DNA as described below, and several different strains wereconstructed to analyze the impact of the addition of these genes onmethionine production. The homocysteine synthase from Corynebacteriumglutamicum and Saccharomyces cerevisiae were also cloned and tested.Both pathways were demonstrated to work simultaneously and methionineproduction was improved with this addition.

To evaluate whether the L. meyeri metX and metY enzymes could complementthe growth of an E. coli methionine auxotroph, the L. meyeri metYX genecluster was amplified from plasmid metXY-pCR2.0-TOPO and cloned into thepPRO-Nde-del vector. The transcription of the metYX genes in thisplasmid was initiated by a lac/ara promoter located on the vector.

Four E. coli strains including W3110 ΔmetA (stopping production ofOSHS), TF4076BJF (increased homoserine production), TF4076BJF ΔmetA(stopping production of OSHS), and TF4076BJF ΔmetAmetB (stoppingproduction of OSHS and cystathionine from OAHS or OSHS) were evaluated.Strain TF4076BJF is a threonine auxotroph, deregulated for methionineproduction with an increase carbon flux up to homoserine, which is ableto produce methionine through the natural E. coli pathway.

The strains were transformed with the cloning vector and the plasmidcontaining metYX, respectively. The transformants were then streakedonto M9 minimal medium plates containing glucose (2 g/L), isoleucine(0.15 g/L), threonine (0.3 g/L), kanamycin (50 mg/L), and IPTG. ThemetYX gene cluster from Leptospira meyeri complemented the growth ofW3110 ΔmetA within 24 hrs. The W3110ΔmetA strain expressing only metXwas not able to grow on the M9 minimal plate. Therefore, E. coli W3110lacks an efficient enzyme to use O-acetyl-L-homoserine as the precursorfor methionine biosynthesis. Strain W3110ΔmetA transformed with thecontrol empty vector, pPRO-Nde-del, as described in WO2006113897, didnot grow within 48 hrs. Strain TF4076BJF grew on the minimal mediumplates when transformed with either the cloning vector or the plasmidcontaining metYX from L. meyeri.

Alternative metYX genes were also tested for growth complementation inminimal medium. In cloning the metYX genes from D. radiodurans, C.aurantiacus, B. linens, N. punctiforme, the translation of the metX genewas coupled with the translation of the metY gene initiated by a rbslocated on the vector, due to the absence of an efficient E. coliribosomal binding site (rbs) adjacent to the downstream gene, metX.

The metYX gene cluster from L. meyeri, D. radiodurans and C. aurantiacuswere the most efficient in complementing the growth of the methionineauxotrophic strains. The complementation of growth was also observed ina methionine auxotroph where metY (L. meyeri) was replaced with the metY(P. aeruginosa) in the L. meyeri metYX gene cluster. These cells showeda reduced growth rate relative to the same methionine auxotrophexpressing the L. meyeri metYX.

Methionine production was determined using the shake flask protocoldescribed in Example 3. Briefly, cultures were grown at 30° C. for 50hours in the medium supplemented with 150 mg/L of methionine (to improveinitial growth) and methionine was measured by HPLC. Table 2 shows thatthe production of methionine was higher in the strains that carried bothpathways compared to those where only the transsulfurylation or thedirect sulfhydrylation was available.

TABLE 2 Methionine Production Methionine Glucose Produced used(final-initial) Strain OD g/L mg/L TF4076BJF 8.2 40.0 439 TF4076BJFmetYX(Lm) 10.2 36.5 984 TF4076BJF metY(Pa)metX(Lm) 9.2 29.1 299TF4076BJF metYX(Dr) 8.8 40.0 510 TF4076BJF metYX(Ca) 12.1 40.0 740TF4076BJF ΔmetA metYX(Lm) 5.8 23.6 368 TF4076BJF ΔmetA metY(Pa)metX(Lm)6.6 21.1 79 TF4076BJF ΔmetAB metYX(Lm) 6.2 23.7 280 TF4076BJF ΔmetABmetYX(Dr) 6.6 32.6 140

Genes metA, and metB are needed for the synthesis of methionine in E.coli strains. When either one of the genes is inactivated, E. coli losesde novo methionine production capability. The data above indicate thatthe addition of the metYX operon restores methionine production tolevels similar to those obtained with a methionine prototroph.Methionine production was in some cases more than double when bothpathways are available to the cell. These results demonstrate that thepathways are not mutually exclusive and that homoserine is converted tomethionine via both routes.

To further demonstrate the benefits of the dual pathway, the strainswere compared in 5 Liter fermentation vessels using the fermentationprotocol described in Example 3. Methionine accumulation started afterapproximately 24 hours and continued until the feed was stopped. Theenzyme coded by the metY gene from most organisms is feedback inhibitedby high concentrations of methionine. In some cases, the enzyme coded bythe metX gene is also feedback inhibited. As a result, significantaccumulation of homoserine and OAHS were observed in thesefermentations. A comparison of methionine production in fermentors isshown in FIG. 2 and the data are summarized in Table 3. These resultsconfirmed the observation seen in the flasks, that the production ofmethionine could be enhanced significantly by the adequate expression ofa heterologous direct sulfhydrylation pathway, and that this pathwaycould be responsible for the majority of the methionine production ifthe enzymes were properly expressed.

TABLE 3 Heterologous expression of direct sulfhydrylation pathwayMethionine O-Acetylhomoserine Strain accumulation g/L accumulation (g/L)TF4076BJF 2.1 — TF4076BJF metYX(Lm) 4.7 7.7 TF4076BJF metY(Pa)metX(Lm)1.5 20.0 TF4076BJF metYX(Dr) 4.7 32.4 TF4076BJF metYX(Ca) 4.9 20.7TF4076BJF ΔmetA metYX(Lm) 4.1 6.2

To increase the flow of products through to methionine, a metY and ametX that are feedback inhibition resistant can be used. It is alsopossible to regulate the level of expression of metX and the expressionof metH to drive the homoserine faster to methionine.

The differences in methionine production indicate that the metXY pathwayis highly effective in E. coli and that the metXY pathway added to aderegulated strain such as this can result in more than double theaccumulation of methionine.

Example 2 Homocysteine Synthase that Utilizes Either O-AcetylL-Homoserine (OAHS) or O-Succinyl L-Homoserine (OSHS)

This example describes methods used to isolate a homocysteine synthaseencoded by metY from Pseudomonas aeruginosa (ATCC 47085). This enzyme isinhibited by both L-methionine and S-adenosyl L-methionine. The enzymeactivity was analyzed according to Yamagata, Methods in Enzymology,143:478, 1987. The method was slightly modified in that multiple samplespoints were taken, guanidine was used to quench the reaction and theformation of homocysteine was detected using DTNB((5,5-Dithiobis(2-nitrobenzoic acid) Sigma D8130) as in the analysis formetA described in Example 3.B. One enzyme unit (U) was defined as theformation of one μmole of homocysteine per minute at room temperature.

MetY from P. aeruginosa was expressed and analyzed using 17.5 μg ofpurified protein (N-tagged). In contrast to the metY from L. meyeri andto most other published homocysteine synthases, this enzyme was activewith both acetyl and succinyl-homoserine. The activity was similar forboth substrates, it was feedback inhibited by methionine and SAMe andthe level of feed back inhibition seemed to be slightly lower when OSHSwas the substrate. Some inhibition was observed at 1 mM methionine. WithOAHS as substrate, at 10, 50 and 100 mM the enzyme retained about 50%,19% and 9%, respectively, of the activity it had in the absence ofmethionine. The activity in the presence of 5 and 10 mM SAMe wasapproximately 72% and 21% of the original activity. When OSHS was thesubstrate the activity dropped to 53% and 31% in the presence of 50 and100 mM methionine and 86% and 19% in the presence of 5 and 10 mM SAMe.

Example 3 Methods of Genetically Engineering Host Stains to Increase theProduction of Methionine

In addition to adding methionine biosynthetic pathways to host organismsas described above in Example 1, the host organism can be furthergenetically engineered to decrease methionine biosynthetic pathwayinhibition, increase reactant availability, and/or decrease productcatabolism.

A. Inactivation of Methionine Global Repressor and Threonine KinaseTogether with Enhanced Expression of 5,10-Methylene-TetrahydrofolateReductase to Increase Methionine Production.

One method of making a methionine production strain is to modify astrain that has already been engineered to produce an amino acid, suchas threonine. For example, the threonine producing strain TF 4076,described in Korean Pat. Publication No. 92-8365 (KFCC 10718) can beused, even though it is a methionine auxotroph). Additional examplestrains include those deposed in ATCC (13070, 13071, 21148, 21149,21150, 21151, 21272, 21277, 21278, 21318, 21319, 21320) that aredescribed as threonine overproducers.

Using strain TF 4076 as a starting point, methionine production wasenhanced by deleting the thrB gene to avoid threonine production anddeleting the metJ gene to release the repression of the expression ofthe methionine biosynthetic pathway. The strain was also modified tooverexpress the metF gene.

thrB Deletion

thrB was deleted using a loxP-chloramphenicol (loxP-Cm) cassette (Gene2000 vol. 247, p 255-264). The thrB gene was cloned by PCR using primersequences 1 and 2 (SEQ ID NOS: 5 and 6) using the chromosome from E.coli K12 as a template. PCR conditions of 94° C. for 30 seconds; then 25cycles of 94° C. for 30 seconds, 55° C. for 30 seconds, and 72° C. for 3minutes; and 72° C. for 7 minutes, with HL PCR premix (Bioneer Co,Korea) were used. PCR products were gel eluted and cloned into thepCR2.1-topo cloning kit (Invitrogen, USA) and named pCR-thrB, pCR-thrBwas digested using pflMI and the loxP-Cm cassette was inserted. Fromthis plasmid, the thrB gene containing loxP-Cm cassette was PCRamplified using primers 1 and 2 (SEQ ID NOS: 11 and 12). The PCRproducts were gel purified. The PCR fragments were electroporated intothe TF4076 strain and chloramphenicol resistant colonies were selectedand confirmed for thrB deletion. The chloramphenicol marker was removedfrom an identified colony and the final strain obtained was namedTF4076B. This strain did not grow on M9 minimal medium (DIFCO) withoutthreonine, indicating that this strain is a threonine auxotroph.

1. thrB SEQ ID NO: 11 5′- GCT AGC c atg gtt aaa gtt tat gcc ccg - 3′2. thrB SEQ ID NO: 12 5′- GAO CTC tta gtt ttc cag tac tcg tgc gc - 3′

MetJ Deletion

To delete the methionine global repressor metJ gene, the FRT one stepdeletion method was used (Datsenko and Wanner PNAS 97:6640-6645, 2000).PCR fragments were amplified using primer sequences 3, 4 (SEQ ID NOS: 13and 14) and template pKD3 (see, Datsenko and Wanner, PNAS 97:6640-6645,2000). The PCR conditions used were 94′C for 30 seconds; followed by 25cycles of 94° C. for 30 seconds, 55° C. for 30 seconds, and 72° C., for1 minute; then 72° C. for 7 minutes, with HL PCR premix (Bioneer Co.,Korea). Chloramphenicol resistant colonies were selected and the metJgene deletion was confirmed using PCR primer sequences 5 and 6 (SEQ IDNOS: 15 and 16). Using pCP20 plasmid transformation, the chloramphenicolmarker gene was removed and the removal was confirmed using PCR. Thestrain obtained was named as TF4076BJ.

3. metJ + chloramphenicol SEQ ID NO: 135′-atggctgaat ggagcggcga atatatcagc ccatacgctg agcacggcaaggtgtaggct ggagctgctt c-3′ 4. metJ + chloramphenicol SEQ ID NO: 145′-gtattcccac gtctccgggt taatccccat ctcacgcatg atctccatat gaatatcctccttag-3′ 5. metJ SEQ ID NO: 15 5′-gggctttgtc ggtgaaatg-3′ 6. metJSEQ ID NO: 16 5′-actttgcgat gagcgagag-3′

MetF Integration

To complement the methionine auxotrophy of TF4076BJ, the metF gene wasexpressed in strain TF4076BJ. The metF gene was amplified using primersequences 7 and 8 (SEQ ID NOS: 17 and 18) and the chromosome of E. coliK12 strain as the template. PCR conditions of 94° C. 30 seconds, then 25cycles of 94° C. 30 seconds, 55° C. 30 seconds, 72° C. 1 minute, andthen 72° C. 7 minutes and HL PCR premix (Bioneer Co., Korea) were used.PCR fragments were gel eluted and inserted into the NheI and SacI sitesin the pSE380 vector (Invitrogen Co.). The plasmid was namedpSE380-metF. pSE380-metF was transformed into the TF4076BJ strain. Thetransformant grew on M9 minimal medium (Difco) containing threonine andisoleucine indicating the complementing of methionine auxotrophy.

The expression level of the metF gene under the control of two differentpromoters was determined. The promoters were the pCJ1 promoter(PCT/KR2005/004338) and the pThreonine promoter. The metF gene wasamplified using primer sequences 9 and 10 (SEQ ID NOS: 19 and 20) andthe chromosome of Escherichia coli K12 strain as the template. PCRconditions of 94° C. 30 seconds, then 25 cycles of 94° C. 30 sec, 55° C.30 sec, 72° C. 1 min, and then 72° C. 7 min and HL PCR premix (BioneerCo., Korea) were used. PCR fragments were gel eluted and ligated intothe PvuII and HindIII sites in the pCL1920 vector (Lerner and Inouye,Nucleic acids Research 18:4631, 1990) containing the pCJ1 promoter orthe pThreonine promoter. The pCJ1 promoter was PCR amplified usingprimer sequences 11 and 12 (SEQ ID NOS: 21 and 22) and the pThreoninepromoter was amplified from the E. coli K12 chromosome using primersequences 13 and 14 (SEQ ID NOS: 23 and 24). The PCR fragments were geleluted and integrated into the KpnI and EcoRV sites in the pCL1920vector. The PCR conditions used were the same as above. The plasmidcontaining the metF gene under the control of the pCJ1 promoter wasnamed pCL-pCJ1-metF and the plasmid containing the metF gene under thecontrol of the pThreonine promoter was named pCL-pThr-metF. Each plasmidwas transformed to TF4076BJ strain and methionine production wasmeasured.

A shake flask culture protocol was used to test the strains as follows:a seed culture was incubated at 31° C. for 6 hrs in medium consisting of(in 1 L): 10 g Yeast extract, 6 g Na₂HPO₄.12H₂O, 0.5 g NaCl, 3 g KH₂PO₄,2 g glucose, 0.49 g MgSO₄.7H2O, 0.015 g CaCl₂.2H₂O. It was then used toinoculate flasks with the following medium: (1 L): 17 g (NH₄)₂SO₄, 1 gMgSO₄.7H2O, 2 g Yeast extract, 0.3 g L-threonine, 10 mg MnSO₄.7H₂O, 10mg FeSO₄.7H₂O, 10 mg Zn SO₄, 30 g CaCO₃, 40 g glucose, and 2 g KH₂PO₄ pH7.2. The flasks were incubated for 64 to 72 hours at 31° C. with shakingat 250 rpm. After centrifugation, culture supernatant was isolated andused for methionine analysis.

For the culture of cells containing the pSE380-metF plasmid, 100 μg/Lampicillin and 0.5 mM IPTG was added in the media. The metF gene underthe control of the pCJ1 promoter produced the most methionine as shownin Table 4.

TABLE 4 Methionine production in cells containing various metFexpression cassettes glucose used OD (g/L) Methionine (mg/L) TF4076BJ7.8 34 0 TF4076BJ/pSE380-metF 5.4 29 130 TF4076BJ/pCL-pCJ1- 7.4 35 206MetF TF4076BJ/pCL-pthr-MetF 22 40 136

To express the metF gene more stably, metF genes under pTrc, pCJ1, andpThreonine promoters were integrated into the lacZ locus of the TF4076BJchromosome. Each metF gene was PCR amplified from each plasmid andinserted into the NsiI site in the pBrint vector (Borgne et al., Gene223:213.219, 1998). The vectors were transformed into the TF4076BJstrain and a transformant that grew on media containing chloramphenicolat 37° C. was selected and confirmed for metF gene integration into theLacZ locus of the chromosome. Selected colonies were transformed bypJW168 and the chloramphenicol marker was deleted. The cells containingpCJ1-metF gene could not be obtained and the transformant containingpThr-metF cassette did not grow well. Only the cells containingpTrc-metF gene in the LacZ locus grew well. The flask culture of thisstrain showed ˜600 mg/L methionine production in the presence of 0.5 mMIPTG in the media. The final strain containing pTrc-metF gene was namedas TF4076BJF and was further analyzed.

In summary, the TF4076BJF strain was derived from threonine-producingstrain TF 4076, which was modified by the deletion of thrB and metJ, andthe insertion of metF under the control of the pTrc promoter. Table 5shows the production of homoserine and methionine by TF4076BJF.

TABLE 5 Methionine production of the strain TF4076BJF Glucose usedHomoserine Methionine Strain OD (g/L) production (g/L) production (g/L)TF4076BJ 15.3 24.7 0.62 0 TF4076BJF 10.6 34.7 4.2 0.64

7. metF SEQ ID NO: 17 5′- GCT AGC c atgagcttttttcacgccag - 3′ 8. metFSEQ ID NO: 18 5′- GAG CTC ttataaaccaggtcgaaccc - 3′ 9. metFSEQ ID NO: 19 5′- CAGCTGatgagctatttcacgccag- 3′ 10. metF SEQ ID NO: 205′- AAGCTT ttataaaccaggtcgaaccc- 3′ 11. CJ1 promoter SEQ ID NO: 215′- cgg ggt acc acc gcg ggc tta ttc cat tac at- 3′ 12. CJ1 promoterSEQ ID NO: 22 5′- acg cga tat ctt aat ctc cta gat tgg gtt tc- 3′13. threonine promoter SEQ ID NO: 235′- cgg ggt acc tgg tta caa caa cgc ctg g- 3′ 14. threonine promoterSEQ ID NO: 24 5′- cat gat atc tac ctcg tta cc ttt ggt cg- 3′

Strain TF4076BJF was grown in 5 L fermentors according to the protocoldescribed below, and a production of approximately 2.2 g/L of methioninewas obtained in 96 hrs.

5 L fermentations were performed using the following protocol. Tocompare the effect of the different genes cloned in the E. coli strain,a basic fermentation protocol for 5 Liter jars was used. The inoculumwas grown in 25 mL of medium consisting of 10.0 g yeast extract, 4.49 gNa₂HPO₄.7H₂O, 0.5 g NaCl, 3.0 g KH₂PO₄, 0.49 g MgSO₄.7H₂O, 0.015 gCaCl₂.2H₂O, and 2 gel, glucose in 1 L volume. 50 mg/L of the appropriateantibiotic was used depending on the resistance of the strain beingtested. After incubation with shaking at 31° C. and 250 rpm for 8-24hours, the culture was transferred to 200 mL of the same medium andincubated under the same conditions for 16 to 20 hours. This culture wasused to inoculate fermentors with 2.5 L of medium.

The fermentation medium consisted of: 17.0 gel, (NH₄)₂SO₄, 2.0 g/L yeastextract, 2.0 g/L KH₂PO₄, 1.0 g/L L-threonine, 0.3 g/L isoleucine, 0.01g/L MnSO₄—H₂O, 0.01 g/L FeSO₄-7H₂O, 0.01 g/L ZnSO₄.7H₂O, 1.0 g/LMgSO₄.7H₂O, 2 mg/L piridoxal, 2 mg/L vitamin B12 and 40 g/L glucose.Antibiotics and IPTG were added depending on the strain being grown. Thefermentation temperature was maintained at 31° C., the dissolved oxygenabove 30% of saturation and the pH was initially controlled with 28%NH₄OH. After the glucose was exhausted, the pH would rise. At thatpoint, a continuous fixed feed would be started, or 100-150 mL aliquotsof feed would be added at a time, based on increases in pH. The feedconsisted of 4.0 g/L yeast extract, 33 g/L (NH₄)₂SO₄, 3.0 g/L KH₂PO₄,1.5 g/L L-threonine, 1.0 g/L MgSO₄-7H₂O, 2 mg/L, vitamin B12 and 400 g/Lglucose. Some minor variations to the medium and feed were introduceddepending on the strain. The fermentation proceeded for a total of 72 to96 hours. Methionine concentration was measured throughout, as well ascell growth by optical density and glucose utilization.

B. Generation of Feedback-Resistant Homoserine Succinyltransferases forMethionine Production

An E. coli strain was constructed with the metA and the metB genesdeleted. This strain showed homoserine accumulation due to the loss ofMetA activity. When the wild-type metA cassette was expressed in thisstrain, OSHS was produced by MetA activity in the absence of methionine.However, when methionine was added in the media, the strain with wt-metAcassette accumulated homoserine again due to the feedback inhibition ofMetA activity. Thus, feed back resistant metA genes can be identified bytesting for O-succinyl homoserine accumulation in the presence ofmethionine. The mutant producing more OSHS in the presence of highamount of methionine in the media contains the most feed-back inhibitionresistant metA.

A Schematic Representation of the Screening Methodology is Provided inFIG. 3.

Construction of metB Deletion Mutant

To make a metB deletion mutant in TF4076BJF, the FRT one step deletionmethod was used (Datsanko and Wanner, PNAS 97:6640-6645, 2000). PCRfragments were amplified using primer sequences 15 and 16 (SEQ ID NOS:25 and 26) and template pKD3 was electroporated into TF4073BJF cells.The PCR conditions of 94° C. 30 seconds, 25 cycles of 94° C. 30 seconds,55° C. 30 seconds, 72° C. 1 minutes, then 72° C. 7 min and HL PCR premix(Korea, Bioneer Co) were used. Chloramphenicol resistant colonies wereselected and confirmed for metB gene deletion using PCP. Thechloramphenicol marker gene was removed using pCP20 plasmidtransformation, and the removal was confirmed by PCR. The strainobtained by this procedure was named as TF4076BJF-B.

15. metB + chloramphenicol SEQ ID NO: 255′-TTACTCTGGT GCCTGACATT TCACCGACAAAGCCCAGGG AACTTCATCA Cgtgtaggct ggagctgctt c -3′ 16. metB +chloramphenicol SEQ ID NO: 26 5′-TTACCCCTTG TTTGCAGCCC GGAAGCCATTTTCCAGGTCG GCAATTAAA Tcatatgaat atcctcctta g -3′

Construction of MetA Deletion Mutant

To make a metA deletion mutant in TF4076BJF-B, the FRT one step deletionmethod was used (PNAS. 97:6640-6645, 2000). PCR fragments were amplifiedusing primer sequences 17, 18 (SEQ ID NOS: 27 and 28) and template pKD3was electroporated into TF4073BJF-B cells. The PCR conditions of 94° C.30 seconds, 25 cycles of 94° C. 30 seconds, 55° C. 30 seconds, 72° C. 1minute, then 72° C. 7 minutes and HL PCR premix (Korea, Bioneer Co) wereused. Chloramphenicol-resistant colonies were selected and confirmed formetA gene deletion using PCR. The chloramphenicol marker gene wasremoved using pCP20 plasmid transformation, and the removal wasconfirmed by PCR. The strain obtained by this procedure was named asTF4076BJF-BA.

17. metA + chloramphenicol SEQ ID NO: 275′-CAATTTCTTGCGTGAAGAAAACGTCTTTGTGATGACAACTTCTCGTGCGTgtgtaggctggagctgcttcc -3′ 18. metA + chloramphenicolSEQ ID NO 28 5′-AATCCAGCGTTGGATTCATGTGCCGTAGATCGTATGGCGTGATCTGGTAGcatatgaatatcctccttag-3′

Construction of MetA Expression Vector

To make a metA library, a metA expression vector was constructed. ThemetA gene was amplified using primer sequences 19 and 20 (SEQ ID NOS: 29and 30) with the chromosome from the E. coli K12 strain as the template.The PCR conditions of 94° C. 30 seconds, 25 cycles of 94° C. 30 seconds,55° C. 30 seconds, 72° C. 1 minute, then 72° C. 7 minutes and HL PCRpremix (Korea, Bioneer Co) were used. The PCR fragments were gel elutedand ligated into pCL1920 at the SmaI site. The plasmid was named pA-CL.The pA-CL plasmid was transformed into the TF4076BJF-AB strain and flaskculture was performed with and without methionine. OSHS and homoserinewere measured by the same method as described above for methionine. Asshown in Table 6, the cells containing the pA-CL plasmid in the absenceof methionine produced 3.8 g/L OSHS with 0.24 g/L homoserine. However,in the presence of 1 g/L methionine the cells produced 5.8 g/L OSHS with4.9 g/L homoserine. The increase of OSHS amount is due to the increaseof growth by methionine addition, while the increase of homoserine isdue to the feed-back inhibition of metA activity by methionine.

TABLE 6 O-succinyl homoserine and homoserine production in TF4076BJF-ABstrain containing pA-CL plasmid Glucose OSH HS Methionine usedproduction production addition Strain OD (g/L) (g/L) (g/L) 0 g/LTF4076BJF-AB/ 2.2 14.2 0 1.42 pCl1920 0 g/L TF4076BJF-AB/ 2.1 13.1 3.80.24 pA-CL 1 g/L TF4076BJF-AB/ 4.7 39.8 0 5.7 pCl1920 1 g/LTF4076BJF-AB/ 6.4 37.4 5.9 4.9 pA-CL

19: metA  SEQ ID NO: 29 5′-aatggatccTGCCGTGAGCGGCGAATAC-3′ 20: metASEQ ID NO: 30 5′-agctctagaCTGCTGAGGTACGTTTCGG-3′Construction of pA-CL Mutant Library

To make a pA-CL mutant library, error-prone PCR was performed.Error-prone PCR was done using the primer sequences 21 and 22 (SEQ IDNOS: 31 and 32) with the pA-CL plasmid as a template. The PCR conditionsof 94° C. 30 seconds, 25 cycles of 94° C. 30 seconds, 55° C. 30 seconds,68° C. 2 minutes, then 72° C. for 7 minutes and BD diversify PCRmutagenesis kit (BD, USA) were used. PCR fragments were digested byBamHI and XbaI and ligated into pCL1920. The library was transformedinto strain TF4076BJF-AB and ˜30,000 transformants were collected forfurther analysis.

21: pCL1920 SEQ ID NO: 31 5′-CGAAGTAATCGCAACATCCG-3′ 22: pCL1920SEQ ID NO: 32 5′-GTCTGCTATGTGGTGCTATC-3′

Preparation of MetB Enzyme Crude Extract

To measure the OSHS by enzymatic method, the MetB enzyme from E. coliwas used. The MetB enzyme reacts with OSHS and cysteine in a 1:1 ratioand produces cystathionine. The reagent DTNB(5,5-Dithiobis(2-nitroberizoic acid) Sigma D8130) reacts with the freeSH group of cysteine and makes a yellow color which can be measured at415 nm. Before the MetB reaction, cysteine reacts with DTNB and turns toyellow color. After the MetB reaction, cysteine turns to cystathioninewhich can not bind to DTNB. By the decrease of OD at 415 am after thereaction, the amount of OSHS in the reaction mix can be measured.

For the overexpression of MetB enzyme, the PCR amplified metB gene fromE. coli K12 chromosome was digested by BamHI and HindIII and cloned intothe pCDF-Duet vector (Novagene, USA). A PCR reaction was performed usingthe primer sequences 23 and 24 (SEQ ID NOS: 33 and 34) and the E. coliK12 chromosome as the template. The PCR conditions of 94° C. 30 seconds,25 cycles of 94° C. 30 seconds, 55° C. 30 seconds, 72° C. 1 minute, then72° C. 7 minutes and HL premix (Bioneer, Korea) were used. The plasmidcontaining the metB gene was transformed into E. coli using a Tuner cell(Novagen, USA) and the transformant was grown overnight with LB mediacontaining 50 μg/mL spectinomycin. The overnight culture broth wasdiluted in LB media containing 50 μg/mL spectinomycin and incubated at37° C. until it reached an OD at 600 nm of 0.6, at which point IPTG wasadded to a final concentration of 0.2 mM and the culture was incubatedfor 4 hrs at 30° C. The cells were harvested by centrifugation at 12,000rpm, resuspended in 0.1 M potassium phosphate buffer (pH 7.5) andruptured by sonication (5×30 seconds). Crude cell extract was acquiredby centrifugation for 20 min at 12,000 rpm and the supernatant was thenused for enzyme assay.

23: metB SEQ ID NO: 33 5′-gccaggatccgATGACGCGTAAACAGGCCAC-3′ 24: mealSEQ ID NO: 34 5′-ccgcaagcttTTTACCCCTTGTTTGCAGCC-3′

Screening of Feed Back Resistant MetA

Feedback resistant metA mutations were identified by inoculating theTF4076BJF-AB strain containing pA-CL mutants into 96 well platescontaining microfermentation media and culturing for 48 hrs at 31° C.with shaking. Microfermentation media is 1 volume of shake flask mediaas described in Example 3, and 1 volume of 0.05M potassium phosphatebuffer pH 6.5, with 5 g/L L-methionine.

The 96 well plates were then centrifuged for 10 min at 3,000 rpm andOSHS was measured in the supernatant by the enzymatic method describedabove (Preparation of MetB crude extract). 50 μL of the culturesupernatant was mixed with 50 μL of reaction buffer (Reaction buffer:0.1 M potassium phosphate buffer (pH 7.5)+2.5 mM cysteine+1/500 10 mMPLP (pyridoxal 5′-phosphate hydrate, Sigma P9255)+1/100 MetB crudeextract (5 mg/mL)). The reaction was incubated for 10 minutes at 37° C.100 μL DTNB (4 mg/10 mL 0.1 M potassium phosphate buffer, pH 7.5) wasadded and the OD at 415 nm was taken. 1 or 2 colonies showing the lowestabsorbance at 415 nm were selected from each 96 well plate and they werestreaked onto LB media containing 50 μg/mL spectinomycin. The resultingcolonies were inoculated onto another 96 well plate containingmicrofermentation media and a second round of screening was performed.The selected strains were then tested under the shake flask cultureconditions described above, with the addition of 5 g/L methionine to themedium, and O-succinylhomoserine production was measured.

24 mutants from 12, 000 colonies were selected for flask culture and 14mutants were selected for sequencing. From those, 5 new mutants wereidentified. The other remaining 9 mutants possessed the same mutationsas had been previously reported. The accumulation of O-SHS andhomoserine in shake flask culture for the 14 mutants is shown in Table7, and the amino acid changes in the metA sequences of the selectedmutants are shown in Table 8.

TABLE 7 Shake flask performance of selected mutants OSH HS Glucoseproduction production Strain No OD used (g/L) (g/L) (g/L) Control 6.0 404.9 5.5 (TF4076BJF-AB/pA-Cl) #7 4.9 40 9.2 2.9 #8 4.6 40 5.4 3.8 #10 4.740 8.8 3.0 #11 4.7 40 9.1 2.8 #32 5.8 40 10.7 1.6 #34 5.6 40 10.1 2.4#36 5.6 40 10.4 2.2 #37 5.9 40 9.6 1.6 #39 7.0 40 9.2 1.0 #22 4.8 40 9.41.4 #23 4.6 40 9.6 1.4 #41 5.6 40 11.8 2.1 #43 6.1 40 11.2 2.3 #47 6.040 11.2 2.2 #49 5.6 40 11.5 2.1

TABLE 8 Sequence analysis of selected mutants 32 37 10 11 41 SEQ IDSEQ ID SEQ ID SEQ ID SEQ ID position wt NO: 2 NO: 4 NO: 6 NO: 8 NO: 10 24 T S (A70T)  29 S P (T85C)  79 N S (A236G) 114 E  G (A341G) 140 F S (T419C) I (T418A) 163 K Q (A487C) 222 F L (T666A) 275 A  E (C824A)290 N H (A868C) 291 Y N (T871A) 295 Q R (A884G) 297 T  A (A889G) 304 ML (A910T) 305 N  Y (A913T) no amino A105G, C222T T450C T915C T573Cacid change A597T

Feed Back Resistance of Mutant MetA

Since all the feed-back inhibition resistant metAs produced similaramounts of OSHS in the presence of 5 g/L methionine in the flaskculture, higher concentrations of methionine were added in the flaskculture media and the production of OSHS was determined. After 64 his ofculture with 30 g/L L-methionine, production of OSHS decreased only inthe #37 mutant sample, and all the others showed similar levels of OSHSproduction as in the presence of 5 g/L methionine. These results,presented in Table 9, indicated that the feed-back inhibition resistancemetAs were resistant to concentrations as high as 30 g/L methionine.

TABLE 9 OSHS production of mutant metAs in the presence of 30 g/Lmethionine Glucose OSH HS used production production Strain OD (g/L)(g/L) (g/L) Control (TF4076BJF-AB/pA-Cl) 4.36 38.6 2.7 1.1  # 10 3.333.1 10.6 0.44 # 11 3.5 36.6 11.5 0.22 # 32 3.1 30.2 10.7 0.23 # 37 2.022.0 6.2 0.05 # 41 4.4 40.0 10.5 Not analyzedIn-Vitro Characterization of Mutant metA Proteins

PCR was used to amplify and then clone the live metA mutant genesidentified as pCL-A#10, pCL-A#11 pCL-A#32, pCL-A#37, and pCL-A#41, intothe pET30a vector. All constructs were subjected to DNA sequenceanalysis to confirm the presence of mutations. The genes were clonedwith a C-terminus His tag for enzyme purification. The enzymes wereoverexpressed, purified and the activity was measured in the presence ofdifferent levels of methionine and SAMe, as described by Lawrence, J.Bacteriol., 109:8-11, 1972. The only modifications to the assay werethat multiple points were taken and that the reaction was quenched withguanidine. Table 10 provides a summary of the activity from the variousmutants, and clearly shows that all the mutants were feed-backinhibition resistant when compared to the wild type enzyme and thatmutants #10 and #11 were the most resistant to both methionine and SAMinhibition.

TABLE 10 Characterization of mutant and wild type MetA enzymes #10 #11#32 #37 #41 Specific activity SEQ ID SEQ ID SEQ ID SEQ ID SEQ ID (U/mg)*w.t. NO: 6 NO: 8 NO: 2 NO: 4 NO: 10 control 386  176 479 276 228 315 w/100 mM Met 29 172 451 218 190 232 w/ 300 mM Met — 125 282 — — — w/ 10 mMSAM 11 150 395  78  63 108 % of specific activity retention w.t. #10 #11#32 #37 #41 control 100 100 100 100  100  100  w/ 100 mM Met 7.6 97 9479 83 74 w/ 300 mM Met — 70 56 — — — w/ 10 mM SAM 2.9 85 82 28 27 34*Where U is the formation of 1 μmole of CoA per minute at roomtemperature

Mutants metA#10 and metA#11 (SEQ ID NOS: 5 and 7, respectively) wereselected for further analysis. metA mutants #10 and #11 were analyzedfor their lack of inhibition in an experiment using 300 mM ofmethionine. This is close to the highest concentration achievable in theassay conditions. The solubility of methionine in water is 5.6 g/100 mLat 30° C., which corresponds to a concentration of 375 mM. In thepresence of 300 mM of methionine, mutant metA#10 retained 70% of itsspecific activity, and mutant metA#11 retained 55% of its specificactivity. Thus, the metA#10 and #11 mutants can be used to in amethionine producing microorganism.

Methionine Production with Feedback Inhibition Resistant metA

metA#10 and metA#11 were individually cloned into the methionineproducing strain TF4076BJF. MetA#10 was also cloned together with metYXfrom L. meyeri. The clones were tested following the fermentationprotocol described in Example 3A. Methionine concentrations wereassessed after 78 hours of fermentation and the results are shown inTable 11. There was no O-succinylhomoserine accumulation in any of thefermentations. The time courses of methionine production are shown inFIG. 4.

TABLE 11 Methionine Accumulation Strain Final methionine titer (g/L)TF4076BJF 2.1 TF4076BJF metA#10 6.3 TF4076BJF metA#11 4.5 TF4076BJFmetA#10 + metYX (Lm) 6.6

These results show that expression of feedback inhibition resistantmetAs increased methionine production and that the combination of adirect sulfhydrylation pathway and a feedback inhibition resistantmetABC pathway showed less synergy than observed with the native MetA.The less synergy observed indicates that the accumulation of methioninemay be inhibiting MetY. To increase methionine production further, afeedback inhibition resistant MetY can be used.

C. Strategies for Attenuation of MetK Activity in E. coli

As described above, the formation of SAMe decreases the concentration ofmethionine and reduces the activity of the methionine biosyntheticpathway via feed back inhibition of metA.

Isolation of mutants in the metK gene are facilitated by the observationthat some ethionine-resistant mutants have reduced levels of metK andoverproduce methionine. Table 12, lists various metK mutations that havebeen described as causing a decrease in MetK activity. These mutantswere constructed as described below.

The metK gene from E. coli (Accession number AP_(—)003499 or BAE77005)was cloned and overexpressed with either an N-terminal or a C-terminalHis tag in pET28b vector. Site directed mutagenesis was performed usingthe C-terminal His tagged metK clone to generate the desired mutants.Expression of the mutant metK proteins was confirmed.

The MetK mutants were purified (using the C-terminal His tag) andassayed in vitro. The wild type C-terminal His-tagged MetK protein wasused as a control. The mutants were assayed using a radioactive assay.The assay conditions were as follows:

-   -   Assay Mix:    -   1.0 mL 0.5 M HEPES/KOH, pH 8.0    -   0.5 mL 1.0 M KCl    -   0.2 mL 1.0 M MgCl₂    -   1.0 mL 100 mM ATP (disodium salt, pH 8.0 with KOH)    -   0.1 mL 50 mM methionine    -   0.1 mL NEN [methyl-¹⁴C]methionine    -   6.6 mL H₂O    -   25 mM EDTA pH 8.0 stop for assays.

45 μl of assay mix was added to an Eppendorf tube and 5 μL of enzyme(normalized data shown in Table 13. The reaction was incubated at roomtemperature (or 25° C.) for a desired period (1 to 10 minutes). Thereaction was stopped with the addition of 150 μL, of 25 mM EDTA. 100 μLof the reaction was spotted onto a 2.5 cm diameter Whatman P-81phosphocellulose filter circle (labeled in pencil). The filters werewashed with 3 L of distilled water, air-dried and placed inscintillation vials with aquasol. The emissions were counted using awindow that extends from ¹⁴C to about 0. Assay efficiency and quenchlevels were determined by adding a known amount of counts of pure¹⁴C-SAM and processing through the whole procedure. Backgrounds aretypically <100 cpm (total counts ca. 10⁵ cpm per reaction).

TABLE 12 Normalized Activity Activity (CPM Expected Effect SAMe/μgpurified Residue Position Replacement on SAMe synth Referenceprotein/min)** His 14 Asn Activity reduced J. Biol 7.7 ~104 fold Chem2000 Asp 16 Asn kcat reduction of J. Biol 2.5 ~103 fold Chem 1999 Gly 77Val Expected Markham 6.9 decrease in personal MetK activitycommunication Cys 90 Ala Only 10% of WT J. Biol Same as WT activity Chem1995 Cys 90 Ser Only 10% of WT J. Biol 23.2 activity Chem 1995 Asp 118Asn kcat reduction of J. Biol 1.3 ~103 fold Chem 1999 Val 185 Glu 6.4Xincrease in AEM 2005 4.9 excreted Met over control Asp 238 Asn kcatreduction of J. Biol 1.9 ~103 fold Chem 1999 Cys 239/240 Ala* Only 10%of WT J. Biol Same as WT activity Chem 1995 Lys 245 Met 42,000 fold J.Biol 2.5 lower activity Chem 2000 than WT Asp 271 Ala kcat reduction ofJ. Biol 0.4 (not duplicated) ~103 fold Chem 1999 WT None Cargill 995.4control* BioTDC WT Untagged None Markham 5600 lab *WT control MetKprotein was also C-terminal His tagged for comparison with the taggedmutant metK proteins. An approximately 6-fold decrease in activity wasobserved with the tagged WT MetK protein when compared to untagged MetKprotein activity. **activity for 5 minute reaction time reported

The product of the MetK reaction, SAMe, is a non-competitive inhibitorof MetK. Therefore, reaction kinetics are complicated to analyze and itis expected that the difference between the activities of the wild typeand the mutants is even higher. By understanding the activity of thevarious mutant MetK enzymes a suitable production host can be designed.

D. SAMe Transporter Regulation

S-AdenosylMet (SAMe) serves as the primary methyl group donor in allorganisms, is involved in polyamine biosynthesis and is essential forcell growth. S-adenosyltransferase (MetK, EC 2.5.1.6) catalyzes the onlyknown route for SAMe biosynthesis in E. coli, as this organism cannotuptake SAMe from the growth medium. An alternative to the downregulation of metK as described above is to provide E. coli with theability to uptake SAMe and simultaneously knock-out the metK gene, toreduce or avoid utilization of methionine via that route. Cell growthcan then be controlled by the addition of SAMe to the fermentationmedium.

A Rickettsia high-affinity SAMe transport system has been identified(Tucker et al., J. Bact. 185: 3031-3035, 2003). This SAMe transporterhas K_(T) values of 2-8 μM which is comparable to the values for thetransporter from S. cerevisiae (3.3 μM), P. carnii (4.5 μM), and ratliver (8.9 μM). In addition it has been reported that the RickettsiaSAMe transport system can complement an E. coli metK deletion mutant(Driskell et al., J. Bact. 187:5719-5722, 2005).

The strains W3110 and TF4076BJF were transformed with a plasmidcontaining the SAM transporter mentioned above. The metK gene from W3110was knocked-out and verified by PCR. According to these modifications,the new strain should have been able to grow only in the presence ofSAM, but not without it. However, it continued to grow in both absenceand presence of exogenous SAM.

E. Knock Out of Methionine Uptake Transporters to Increase Methionine inFermentation Medium

Two L-methionine transporters have been, identified in E. coli, one witha very high affinity (Km=0.1-0.13 μM) and a second with lower affinity(Km=20-40 μM). The locus for the high affinity transporter system isdesignated metD since the metD mutants are unable to transportD-methionine and to utilize it as a methionine source. The metD locuscorresponds to the abc (metN), yaeE (metI) and yaeC (metQ) genes whichencode an ABC transporter necessary for L-methionine and D-methionineuptake. metN encodes the putative ATPase and metI encodes themembrane-spanning region of the metD ABC transporter. It is expectedthat the third component, metQ, encodes the substrate-binding domain.Since, metI, metN and metQ deletion mutants can still grow in thepresence of L-methionine, it is taken to be indirect evidence for thepresence of the low affinity metP system.

As illustrated in FIG. 5, metD imports D- and L-methionine, while thegenetically uncharacterized transporter metP imports only L-methionine.MetD is represented as a typical ABC transporter with its threecomponents: A, E, and C represent abc (ATPase), yaeE (permease), andyaeC (D-methionine-binding protein), respectively. (Merlin et al., J.Bacteriol. 184: 5513-5517, 2002).

metJ, the global methionine repressor protein, was shown to negativelycontrol expression of the operon encoding the metD locus. Transcriptionof the metD genes increases upon deprivation of methionine, which is ametJ corepressor. In cells with a metJ deletion, the transporters aremore highly expressed and not repressed by methionine (Merlin et al., J.Bacteriol. 184: 5513-5517, 2002). Methionine productions strainsgenerally have attenuated metJ sequences or metJ deletions so, toincrease production, it can be particularly important to reduce themethionine import activity. The strains can be modified by knocking outthe metD methionine uptake system. This will prevent methionine uptakeand avoid the potential energy-wasting futile cycle of uptake/excretion.

Knocking out metD resulted in a 25% increase in methionine accumulationin the fermentation broth, as measured by the shake flask protocoldescribed in Example 3, above.

F. Over Expression of MetH

The increase in carbon flux through the methionine pathway due to themodifications to the strains described here, can lead to an accumulationof homocysteine inside the cell. Homocysteine is very toxic to the cell.To avoid any accumulation and convert the homocysteine to methionine, itis very important to have very active homocysteine methylase activity(EC 2.1.1.13 and 2.1.1.14) which are codified by the metE and metH,respectively. One way to accomplish this is to overexpress these geneseither in a plasmid system or by placing the chromosomal copy under thecontrol of a strong promoter.

The native metH gene from E. coli was overexpressed under severaldifferent promoters in a strain containing the dual pathways metABC andmetXY, and the methionine production was measured in our standard shakeflask protocol. The three vectors used for meal overexpression werepCL-P(cysK), pCL-P(pro), and pCL-P(CJ-1) which were respectivelymodified from commercially available plasmid pCL1920 by replacing thePlac promoter with the promoter of E. coli cysK gene, the promoter fromcommercial vector pPROLar, and CJ Corporation's proprietary promoterCJ1. The ORF of the E. coli metH gene was located just downstream of thepromoters. The results obtained are shown in Table 13, below. It wasclear that even at the relatively low levels of methionine accumulatedin the shake flask protocol, the presence of a high concentration of thehomocysteine methylase had a very significant positive effect on theproduction of methionine. The effect was even more pronounced infermentors.

TABLE 13 Effect of over-expression of metH on methionine productionGlucose Methionine Strains OD used Produced TF4076BJF met YX Lm 7.4 40.0868 TF4076BJF met YX Lm pcL-P (cysK) 11.7 33.9 1289 met H TF4076BJF metYX Lm pcL-P (pro) 7.5 32.8 1062 met H TF4076BJF met YX Lm pcL-P (CJ-1)12.4 40.0 1337 met H TF4076BJF met YX Dr 10 38.2 569 TF4076BJF met YX DrpcL-P (cysK) 15.4 40.0 896 met H TF4076BJF met YX Dr pcL-P (pro) met H12.5 40.0 786 TF4076BJF met YX Dr pcL-P (CJ-1) 15 40.0 856 met H

G. Improving Sulfate Uptake and Increasing APS Pool in MethionineProducing Organisms

This Example describes a method of engineering E. coli to bypass thehue/mediate, PAPS, in its endogenous sulfur assimilation pathway. Thenew pathway created requires one less molecule of ATP for each sulfatemolecule reduced to sulfide, thus, it is more energy efficient (see,FIG. 6).

As previously described, FIG. 6 shows two ways to take advantage ofalternative sulfur assimilation pathways. One way is to clone theadenylyl sulfate reductase, cysH (EC 1.8.4.9) gene from Bacillus or P.aeruginosa and either incorporate it into the E. coli genome or expressit from a plasmid. This allows APS to be converted to sulfite in asingle step, thus avoiding the conversion of APS to PAPS catalyzed by E.coli APS kinase (cysC). The second way would be to mutate the E. coliPAPS reductase gene, based on the bacterial cysH homologs, so that itssubstrate specificity is changed from PAPS to APS.

The cysH genes from Bacillus subtilis 168 (Accession number AJ000974REGION: 548-1249) and Pseudomonas aeruginosa PAM (Accession numberNC_(—)002516 REGION: 1895692 . . . 1896495) were cloned into plasmidsand tested to determine if they could complement E. coli cysC or cysHknockout mutants, which are auxotrophic for both cysteine andmethionine.

Briefly, the cysH genes from Bacillus subtilis 168 and Pseudomonasaeruginosa PA01 were transformed into BL21(DE3)ΔcysH, a cysH knockout ofBL21(DE3), to test for complementation. Single colonies from thefollowing four strains were used to inoculate 5 mL cultures containingthe Overnight Express medium (OnEX: defined medium supplemented withamino acids but not cysteine or methionine) from Novagen.

Cultures were incubated for 48 hrs at 30° C. with constant shaking. Theresults, presented in Table 14, indicate that both the cysH gene from B.subtilis and P. aeruginosa were able to complement the cysH knockout inE. coli and to sustain growth.

TABLE 14 Optical density at 600 nm of ΔcysH complementation experimentsStrain OD₆₀₀ BL21(DE3) (wild type strain) 5.2 BL21(DE3)ΔcysH (withdeletion of cysH) 0 BL21(DE3)ΔcysH + pET23BscysH (addition of BacilluscysH) 7.2 BL21(DE3) Δ cysH + pET23PacysH (addition of Pseudomonas 6.8cysH)

Similarly, a strain that had the cysC gene knocked out was used to testcomplementation by the B. subtilis and P. aeruginosa cysH genes. StrainBL21(DE3)ΔcysC was transformed with plasmids pET23a, pET23a+cysH (B.subtilis), and pET23a+cysH (P. aeruginosa), respectively. Singlecolonies of the above three strains together with BL21(DE3) wereinoculated in 5 mL of OnEx medium containing amino acids exceptL-cysteine and L-methionine. The cells were cultured at 37° C. withshaking for 48 h and growth was measure by OD_(600nm). The results,showed in Table 15, indicated that cysH-encoded APS reductase from bothB. subtilis and P. aeruginosa could complement the cysC mutation onBL21(DE3) which demonstrated that it was possible to bypass theformation of PAPS.

TABLE 15 Optical density at 600 nm of ΔcysC complementation experimentsstrain OD_(600 nm) ^(a) BL21(DE3) 4.5 BL21(DE3) ΔcysC + pET23a 0.0BL21(DE3) ΔcysC + pET23a + cynH (B. subtilis) 2.5 BL21(DE3) ΔcysC +pET23a + cysH (P. aeruginosa) 4.2 ^(a)The results are the average ofthree cultures.

Overexpression of Enzymes in the Sulfur Assimilation Pathway

As described above, to increase the production of methionine it can behelpful to have a very efficient sulfur assimilation pathway. Tofacilitate direct sulfhydrylation of the acylhomoserine precursor, theavailability of SH₂ is essential. All of the main genes of the sulfurassimilation pathway were cloned and overexpressed in the methionineproduction strain TF4076BJF. The genes overexpressed were:

cys PUWA: sulfate permeasecysDN: ATP sulfurylase (EC 2.7.7.4)CysCCysH: APS kinase and PAPS sulfotransferase (EC 2.7.1.25 and EC1.8.4.8)CysIJCysG: NADPH-Sulfite reductase (EC 1.8.1.2)CysB: transcription activator

These genes were overexpressed in a strain containing the dual pathwaysmetABC and metXY, and the methionine production was measured in ourstandard shake flask protocol. The aforementioned five groups of sulfateassimilating genes were respectively cloned into vector pCL-(Prmf) whichwas constructed by replacing the Plac promoter of plasmid pCL1920 withthe promoter of E. coli rmf gene. The results obtained are shown inTable 16 below:

TABLE 16 Results from overexpression of various sulfur assimilationpathway enzymes Strains OD Met mg/L Met/OD TF4076BJF metYX (Lm) 8.0 934116 TF4076BJF metYX (Lm) cysPUWA 4.2 206 49 TF4076BJF metYX (Lm) cysDN10.3 1271 123 TF4076BJF metYX (Lm) cysCcysH 9.9 1348 136 TF4076BJF metYX(Lm) cysJIcysG 7.7 1038 134 TF4076BJF metYX (Lm) cysB 9.4 425 45

Overexpression of the transport enzymes as well as the transcriptionregulator resulted in lower production of methionine and a significantdrop in the amount of methionine per unit of cell mass. Increasing theactivity of the sulfurylase, the APS kinase and the sulfotransferase,all resulted in increased methionine production per unit of cells aswell as total methionine produced. Given that these increases areobserved in a strain harboring two different plasmids, it can beexpected that the results will be improved much further once expressionof the enzymes is tuned and optimized.

Example 4 Exemplary Methionine Production Strains

As previously described, the various genetic modifications describedherein can be made through incorporation of recombinant DNA sequencesindependent of the chromosome, or the recombinant DNA sequences can beincorporated into the production strain chromosome. The recombinant DNAsequences can be incorporated into the host cells as a single copy or inmultiple copies.

i) A microorganism, such as E. coli ATCC #13070 or TF4076, is engineeredto contain a functional deletion of thrB and met so that the genes areattenuated. This microorganism expresses the metX and metY genes, aswell as a recombinant nucleic acid sequence which causes overexpressionof the native metH gene. The expression of metX and metY introduces anadditional pathway in E. coli and the overexpression of the native metHgene causes an increased flux of homocysteine to methionine.

ii) Another production strain is created by making the followingmodifications to the microorganism described in i). The microorganismdescribed in i), is further modified by transforming the microorganismwith a recombinant DNA molecule encoding an active metZ gene, such asthe one from Pseudomonas aeruginosa.

iii) Yet another production strain is created by making the followingmodifications to the microorganism described in i). The microorganismdescribed in i), is further modified to replace the native metA genewith a feedback inhibition resistant metA gene, such as those describedin Example 3.

iv) Another production strain is created by making the followingmodifications to the microorganism described in iii). The microorganismdescribed in iii) is transformed with an active metZ gene.

v) Another production strain is created by making the followingmodifications to the microorganism described in i). The microorganismdescribed in i) which overexpresses the product of the metF gene isadditionally modified to attenuate the transcriptional repressor genelacI.

vi) Additional production strains are created by making the followingmodifications to any of the productions strains described herein. Theproduction strains are engineered to overexpress the genes cysDN, cysIJ,or cysCH or combinations thereof to improve sulfur assimulation.Optionally, these production strains are additionally modified toreplace the native cysC and cysH from E. coli with a single cysH genefrom P. aeurignosa or B. subtilis.

vii) Another production strain is made by modifying any of theproduction strains described herein such that the methionine importergene metD is attenuated.

What is claimed is:
 1. A microorganism comprising: one or more firstpeptides comprising direct sulfhydrylation activity (EC 2.5.1.49 and4.2.99.-, wherein the direct sulfhydrylation activity uses as asubstrate OSHS or OAHS; and one or more second peptides comprisingtranssulfuration activity (EC 2.5.1.48, and 4.4.1.8, wherein the directsulfhydrylation activity consists of expression from an exogenousnucleic acid sequence.
 2. The microorganism of claim 1, wherein themicroorganism is E. coli.
 3. The microorganism of claim 1, furthercomprising detectable amount of methionine.
 4. The microorganism ofclaim 1, further comprising detectable amount of SAMe.
 5. Themicroorganism of claim 3, wherein at least 10% of the methionineproduced is from transsulfuration activity.
 6. The microorganism ofclaim 4, wherein at least 10% of the SAMe produced is fromtranssulfuration activity.
 7. The microorganism of claim 3, wherein atleast 10% of the methionine produced is from direct sulfhydrylationactivity.
 8. The microorganism of claim 4, wherein at least 10% of theSAMe produced is from direct sulfhydrylation activity.
 9. Themicroorganism of claim 1, further comprising a homoserineO-succinyltransferase peptide that is feed back resistance.
 10. Themicroorganism of claim 1, further comprising a homoserineO-succinyltransferase peptide with GenBank Accession No: AAC76983 thathas mutations in amino acid position 24, 29, 79, 114, 140, 163, 222,275, 290, 291, 295, 297, 304, 305, or combinations thereof.
 11. Themicroorganism of claim 1, further comprising a homoserineO-succinyltransferase peptide that comprises SEQ ID NOS: 2, 4, 6, 8, or10.
 12. The microorganism of claim 1, further comprising an exogenousnucleic acid sequence encoding an adenylyl sulfate reductase (EC1.8.99.2).
 13. The microorganism of claim 1, wherein at least one geneselected from metD, metK, metJ, thrB, serA or combinations thereof isattenuated.
 14. The microorganism of claim 1, wherein at least one geneselected from metA, metB, metC, metE, metY, metZ, metX, metH, cysPWUA,cysD, cysN, cysC, cysH, cysI, cysJ, cysG, csyK, cysM, and combinationsthereof, is over-expressed.
 15. A method of making methioninecomprising: culturing the microorganism of claim 1 under conditions thatpermit production of methionine; and isolating the methionine.
 16. Themethod of claim 15, wherein the first peptide having directsulfhydrylation activity is encoded by metZ, metY or combinationsthereof.
 17. The method of claim 15, wherein the microorganism is E.coli.
 18. The method of claim 16, wherein at least 10% of the methionineis produced from the first peptide and wherein the first peptide isencoded by metZ, metY or combinations thereof.
 19. The method of claim15, wherein at least 10% of the methionine is produced from the secondpeptide and wherein the second peptide is encoded by metB, metC orcombinations thereof.
 20. The method of claim 15, wherein the endogenoustranssulfuration activity is encoded by metB, metC or combinationsthereof.
 21. The method of claim 1, wherein at least 10% of themethionine produced is produced from the first peptide and wherein thefirst peptide is encoded by a metZ gene.
 22. The microorganism of claim1, wherein the first peptide is a MetX peptide comprising an amino acidsequence having at least 70% sequence identity to accession numbersCAA71733, ZP_(—)00766367 or ZP_(—)00107218.
 23. The microorganism ofclaim 1, wherein the first peptide is a MetX peptide comprising an aminoacid sequence having at least 90% sequence identity to accession numbersCAA71733, ZP_(—)00766367 or ZP_(—)00107218.
 24. The method of claim 15,wherein the first peptide is a MetY peptide comprising an amino acidsequence having at least 70% sequence identity to accession numbersAAG08410, CAA71732, ZP_(—)00766366, or ZP_(—)00107219.
 25. The method ofclaim 15, wherein the first peptide is a MetY peptide comprising anamino acid sequence having at least 90% sequence identity to accessionnumbers AAG08410, CAA71732, ZP_(—)00766366, or ZP_(—)00107219.
 26. Themethod of claim 15, wherein the second peptide is a MetZ peptide havingan amino acid sequence comprising at least 70% sequence identity toaccession number AAG06495.
 27. The method of claim 15, wherein thesecond peptide is a MetZ peptide having an amino acid sequencecomprising at least 90% sequence identity to accession number AAG06495.28. The method of claim 15, wherein the microorganism further comprisesan attenuated gene selected from metD, metK, metJ, thrB, serA orcombinations thereof.
 29. The method of claim 15, wherein themicroorganism further comprises additional genetically engineerednucleic acid sequence changes resulting in a genetically engineeredproduction strain, and wherein the genetically engineered productionstrain produces 10% more methionine compared to the microorganismwithout such changes.
 30. The method of claim 29, wherein thegenetically engineered production strain includes a genetic modificationto decrease product catabolism, increase reactant availability, decreasemethionine biosynthetic pathway inhibition or combinations thereof. 31.An isolated E. coli comprising a cystathionine gamma synthase (EC2.5.1.48) or O-succinyl homoserine sulfhydrylase (EC 4.2.99.-) and ahomocysteine synthase (EC 2.5.1.49) expressed from an exogenous nucleicacid sequence.
 32. The isolated E. coli of claim 31, comprising acystathionine gamma synthase (EC 2.5.1.48) expressed from an endogenousnucleic acid sequence and a homocysteine synthase (EC 2.5.1.49)expressed from an exogenous nucleic acid sequence.
 33. The isolated E.coli of claim 32, further comprising homoserine O-acetyltransferase (EC2.3.1.31).
 34. The isolated E. coli of claim 31, wherein the exogenousnucleic acid sequence shares at least 70% sequence identity to anaccession number selected from accession numbers AE004091, AE004091REGION: 5655648 . . . 5656925, Y10744 REGION: 1485 . . . 2813,NZ_AAAH02000004 REGION: 164536 . . . 165990 and NZ_AAAY02000081 REGION:complement (12750 . . . 14054).
 35. The isolated E. coli of claim 31,wherein the exogenous nucleic acid sequence shares at least 90% sequenceidentity to an accession number selected from accession numbersAE004091, AE004091 REGION: 5655648 . . . 5656925, Y10744 REGION: 1485 .. . 2813, NZ_AAAH02000004 REGION: 164536 . . . 165990 andNZ_AAAY02000081 REGION: complement (12750 . . . 14054).
 36. The isolatedE. coli of claim 31, wherein the exogenous nucleic acid sequence isselected from accession numbers AE004091, AE004091 REGION: 5655648 . . .5656925, Y10744 REGION: 1485 . . . 2813, NZ_AAAH02000004 REGION:
 164536. . . 165990 and NZ_AAAY02000081 REGION: complement (12750 . . . 14054).37. The isolated E. coli of claim 31, further comprising an exogenousnucleic acid sequence encoding an adenylyl sulfate reductase (EC1.8.99.2).
 38. A method of making methionine, comprising culturing anisolated microorganism comprising a recombinant DNA molecule, whereinthe recombinant DNA molecule over expresses adenylyl sulfate reductase(EC 1.8.99.2) under conditions sufficient for producing methionine; andisolating methionine.
 39. The method of claim 38, wherein themicroorganism is E. coli.
 40. The method of claim 38, wherein themicroorganism comprises a gene encoding metX, metY, metB, metC, metZ,and combinations thereof.
 41. The method of claim 40, wherein the geneis endogenous.
 42. The method of claim 40, wherein the gene isexogenous.
 43. An isolated peptide comprising a peptide encoded by anucleic acid sequence selected from SEQ ID NOS: 1, 3, 5, 7, or 9,wherein the peptide comprises homoserine O-succinyltransferase activity.